Open Access

The importance of distinguishing pseudogenes from parental genes

Clinical EpigeneticsThe official journal of the Clinical Epigenetics Society20146:33

DOI: 10.1186/s13148-014-0033-5

Received: 28 November 2014

Accepted: 28 November 2014

Published: 31 December 2014

Abstract

No abstract

Dear Editor,

The July-August 2014 issue of Clinical Epigenetics featured a research article describing PTEN promoter hypermethylation in multiple myeloma by Piras et al. [1]. The importance of the PTEN gene has resulted in significant efforts to identify sequence, expression and methylation changes in cancer. Piras et al. concluded that PTEN hypermethylation occurred in a subset of multiple myeloma cases but that hypermethylation did not correlate with reduced gene expression or clinical parameters. The PTEN mRNA shares 97.8% sequence identity with a pseudogene known as PTENP1. A 921-bp region of the promoters of these genes is also 91% identical. Consequently, careful consideration of assay design is required to avoid amplification of PTENP1 rather than PTEN sequences. However, the method used by Piras et al. for measuring PTEN mRNA did not distinguish between these homologues, despite numerous studies showing that PTENP1 mRNA is ubiquitously expressed in both normal and cancer specimens [2]–[5]. Furthermore, previous studies have demonstrated that apparent methylation of the PTEN promoter is likely attributable to the non-specific amplification of the highly homologous PTENP1 gene [6],[7]. We have shown that the only reliable method for distinguishing between PTEN and PTENP1 promoter methylation is single-molecule bisulfite sequencing that utilizes sequence differences between the two genes to separately analyze individual promoter molecules [6],[8]. These methodological challenges make comparisons between methylation and expression impossible when using assays that do not reliably discriminate between PTEN and PTENP1, and also negate the value of correlating these features with clinicopathological characteristics.

The challenges posed by sequence homology with pseudogenes are by no means particular to the PTEN gene. For example, the DNA mismatch repair gene PMS2 shares >95.2% sequence identity with at least six other genes (PMS2CL, PMS2L2, PMS2P4, PMS2P5, PMS2P1 and PMS2P11) making analysis of the PMS2 CpG island promoter region particularly challenging.

In light of the recent manuscript by Piras et al., it is necessary to highlight the importance of rigorous methodology when investigating DNA methylation changes in cancer, especially concerning genes with homologues or pseudogenes such as PTEN.

Declarations

Authors’ Affiliations

(1)
Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW

References

  1. Piras G, Monne M, Palmes a, Calvisi A, Asproni R, Vacca F, Pilo L, Gabbas A, Latte G: Methylation analysis of the phosphates and tensin homologue on chromosome 10 gene (PTEN) in multiple myeloma. Clin Epigenetics. 2014, 6: 16-10.1186/1868-7083-6-16.PubMed CentralView ArticlePubMedGoogle Scholar
  2. Fujii GH, Morimoto AM, Berson AE, Bolen JB: Transcriptional analysis of the PTEN/MMAC1 pseudogene, psiPTEN. Oncogene. 1999, 18: 1765-1769. 10.1038/sj.onc.1202492.View ArticlePubMedGoogle Scholar
  3. Ioffe YJ, Chiappinelli KB, Mutch DG, Zighelboim I, Goodfellow PJ: Phosphatase and tensin homolog (PTEN) pseudogene expression in endometrial cancer: a conserved regulatory mechanism important in tumorigenesis?. Gynecol Oncol. 2012, 124: 340-346. 10.1016/j.ygyno.2011.10.011.PubMed CentralView ArticlePubMedGoogle Scholar
  4. Yokoyama Y, Wan X, Shinohara A, Takahashi S, Takahashi Y, Niwa K, Tamaya T: Expression of PTEN and PTEN pseudogene in endometrial carcinoma. Int J Mol Med. 2000, 6: 47-50.PubMedGoogle Scholar
  5. Zhang CL, Tada M, Kobayashi H, Nozaki M, Moriuchi T, Abe H: Detection of PTEN nonsense mutation and psiPTEN expression in central nervous system high-grade astrocytic tumors by a yeast-based stop codon assay. Oncogene. 2000, 19: 4346-4353. 10.1038/sj.onc.1203795.View ArticlePubMedGoogle Scholar
  6. Hesson LB, Packham D, Pontzer E, Funchain P, Eng C, Ward RL: A reinvestigation of somatic hypermethylation at the PTEN CpG island in cancer cell lines. Biol Proced Online. 2012, 14: 5-10.1186/1480-9222-14-5.PubMed CentralView ArticlePubMedGoogle Scholar
  7. Zysman MA, Chapman WB, Bapat B: Considerations when analyzing the methylation status of PTEN tumor suppressor gene. Am J Pathol. 2002, 160: 795-800. 10.1016/S0002-9440(10)64902-4.PubMed CentralView ArticlePubMedGoogle Scholar
  8. Hesson LB, Ward RL: Discrimination of pseudogene and parental gene DNA methylation using allelic bisulfite sequencing. Methods Mol Biol. 2014, 1167: 265-274. 10.1007/978-1-4939-0835-6_18.View ArticlePubMedGoogle Scholar

Copyright

© Hesson and Ward; licensee BioMed Central. 2014

This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

Advertisement