Format

Send to

Choose Destination
BMC Cancer. 2017 Jul 17;17(1):489. doi: 10.1186/s12885-017-3482-3.

Quantitation of DNA methylation in Epstein-Barr virus-associated nasopharyngeal carcinoma by bisulfite amplicon sequencing.

Author information

1
Department of Environmental and Molecular Medicine, Mie University Graduate School of Medicine, 2-174, Edobashi, Tsu, Mie, 514-8507, Japan.
2
Department of Otorhinolaryngology, Head and Neck Surgery, Mie University Graduate School of Medicine, Tsu, Mie, Japan.
3
Department of Otolaryngology Head and Neck Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, China.
4
Present address: Department of Research, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi, China.
5
Present address: Center for Oral Biology, University of Rochester Medical Center, Rochester, NY, USA.
6
Graduate School of Health Science, Suzuka University of Medical Science, Suzuka, Mie, Japan.
7
Department of Environmental and Molecular Medicine, Mie University Graduate School of Medicine, 2-174, Edobashi, Tsu, Mie, 514-8507, Japan. mmurata@doc.medic.mie-u.ac.jp.
8
Department of Otorhinolaryngology, Head and Neck Surgery, Mie University Graduate School of Medicine, Tsu, Mie, Japan. kazuhiko@clin.medic.mie-u.ac.jp.

Abstract

BACKGROUND:

Epigenetic changes, including DNA methylation, disrupt normal cell function, thus contributing to multiple steps of carcinogenesis. Nasopharyngeal carcinoma (NPC) is endemic in southern China and is highly associated with Epstein-Barr virus (EBV) infection. Significant changes of the host cell methylome are observed in EBV-associated NPC with cancer development. Epigenetic marks for NPC diagnosis are urgently needed. In order to explore DNA methylation marks, we investigated DNA methylation of candidate genes in EBV-associated nasopharyngeal carcinoma.

METHODS:

We first employed methyl-capture sequencing and cDNA microarrays to compare the genome-wide methylation profiles of seven NPC tissues and five non-cancer nasopharyngeal epithelium (NNE) tissues. We found 150 hypermethylated CpG islands spanning promoter regions and down-regulated genes. Furthermore, we quantified the methylation rates of seven candidate genes using bisulfite amplicon sequencing for nine NPC and nine NNE tissues.

RESULTS:

All seven candidate genes showed significantly higher methylation rates in NPC than in NNE tissues, and the ratios (NPC/NNE) were in descending order as follows: ITGA4 > RERG > ZNF671 > SHISA3 > ZNF549 > CR2 > RRAD. In particular, methylation levels of ITGA4, RERG, and ZNF671 could distinguish NPC patients from NNE subjects.

CONCLUSIONS:

We identified the DNA methylation rates of previously unidentified NPC candidate genes. The combination of genome-wide and targeted methylation profiling by next-generation sequencers should provide useful information regarding cancer-specific aberrant methylation.

KEYWORDS:

Bisulfite amplicon sequencing; DNA methylation; Epigenetic mark; Methyl-capture sequencing; Nasopharyngeal carcinoma

PMID:
28716111
PMCID:
PMC5514474
DOI:
10.1186/s12885-017-3482-3
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for BioMed Central Icon for PubMed Central
Loading ...
Support Center