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Open Access Research article

Derepression of Cancer/Testis Antigens in cancer is associated with distinct patterns of DNA Hypomethylation

Robert Kim13, Prakash Kulkarni1* and Sridhar Hannenhalli2*

Author Affiliations

1 James Buchanan Brady Urological Institute, The Johns Hopkins University School of Medicine, 600 North Wolfe Street, Baltimore, MD, 21287, USA

2 Department of Cell Biology & Molecular Genetics, and Center for Bioinformatics & Computational Biology, University of Maryland, 3104G Biomolecular Sciences Building (#296), College Park, MD, USA

3 Present address: Department of Neurology, Yale University School of Medicine, New Haven, CT, USA

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BMC Cancer 2013, 13:144  doi:10.1186/1471-2407-13-144

Published: 22 March 2013

Abstract

Background

The Cancer/Testis Antigens (CTAs) are a heterogeneous group of proteins whose expression is typically restricted to the testis. However, they are aberrantly expressed in most cancers that have been examined to date. Broadly speaking, the CTAs can be divided into two groups: the CTX antigens that are encoded by the X-linked genes and the non-X CT antigens that are encoded by the autosomes. Unlike the non-X CTAs, the CTX antigens form clusters of closely related gene families and their expression is frequently associated with advanced disease with poorer prognosis. Regardless however, the mechanism(s) underlying their selective derepression and stage-specific expression in cancer remain poorly understood, although promoter DNA demethylation is believed to be the major driver.

Methods

Here, we report a systematic analysis of DNA methylation profiling data from various tissue types to elucidate the mechanism underlying the derepression of the CTAs in cancer. We analyzed the methylation profiles of 501 samples including sperm, several cancer types, and their corresponding normal somatic tissue types.

Results

We found strong evidence for specific DNA hypomethylation of CTA promoters in the testis and cancer cells but not in their normal somatic counterparts. We also found that hypomethylation was clustered on the genome into domains that coincided with nuclear lamina-associated domains (LADs) and that these regions appeared to be insulated by CTCF sites. Interestingly, we did not observe any significant differences in the hypomethylation pattern between the CTAs without CpG islands and the CTAs with CpG islands in the proximal promoter.

Conclusion

Our results corroborate that widespread DNA hypomethylation appears to be the driver in the derepression of CTA expression in cancer and furthermore, demonstrate that these hypomethylated domains are associated with the nuclear lamina-associated domains (LADS). Taken together, our results suggest that wide-spread methylation changes in cancer are linked to derepression of germ-line-specific genes that is orchestrated by the three dimensional organization of the cancer genome.

Keywords:
DNA hypomethylation; Cancer/Testis antigens; Lamina attachment domains; Insulator regions