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

• Published in: BMC cancer Vol. 17; no. 1; pp. 489 - 9
• Main Authors: Zhao, Weilin, Mo, Yingxi, Wang, Shumin, Midorikawa, Kaoru, Ma, Ning, Hiraku, Yusuke, Oikawa, Shinji, Huang, Guangwu, Zhang, Zhe, Murata, Mariko, Takeuchi, Kazuhiko
• Format: Journal Article
• Language: English
• Published: London BioMed Central 17.07.2017; BioMed Central Ltd; BMC
• Subjects: Adult; Aged; Biomarkers; Biomedical and Life Sciences; Biomedicine; Biopsy; Bisulfite; Bisulfite amplicon sequencing; Cancer Research; Carcinogenesis; Carcinoma - diagnosis; Carcinoma - genetics; Carcinoma - pathology; Carcinoma - virology; Care and treatment; Cell Line, Tumor; Colorectal cancer; Complications and side effects; CpG islands; CpG Islands - genetics; Deoxyribonucleic acid; Development and progression; Diagnosis, Differential; DNA; DNA methylation; DNA Methylation - genetics; DNA microarrays; DNA sequencing; Epigenesis, Genetic - genetics; Epigenetic mark; Epigenetics; Epithelium; Epithelium - metabolism; Epstein-Barr virus; Epstein-Barr virus diseases; Epstein-Barr Virus Infections - complications; Epstein-Barr Virus Infections - genetics; Epstein-Barr Virus Infections - virology; Female; Gene expression; Genetic aspects; Genetics; Genomes; Genomics; genomics and epigenetics; GTP Phosphohydrolases - genetics; Health aspects; Health Promotion and Disease Prevention; Herpesvirus 4, Human - genetics; Herpesvirus 4, Human - pathogenicity; High-Throughput Nucleotide Sequencing; Humans; Integrin alpha6 - genetics; Male; Medical prognosis; Medicine/Public Health; Methyl-capture sequencing; Middle Aged; Nasopharyngeal cancer; Nasopharyngeal Carcinoma; Nasopharyngeal Neoplasms - diagnosis; Nasopharyngeal Neoplasms - genetics; Nasopharyngeal Neoplasms - pathology; Nasopharyngeal Neoplasms - virology; Nasopharynx - metabolism; Oncology; Penicillin; Proteins; Quantitation; Research Article; Surgical Oncology; Throat cancer; Tumor Suppressor Proteins - genetics; Nasopharyngeal carcinoma; DNA methylation; Bisulfite amplicon sequencing; Epigenetic mark; Methyl-capture sequencing
• ISSN: 1471-2407; 1471-2407
• DOI: 10.1186/s12885-017-3482-3

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.