Characterization of the Nasopharyngeal Carcinoma Methylome Identifies Aberrant Disruption of Key Signaling Pathways and Methylated Tumor Suppressor Genes

Abstract

Aims: Nasopharyngeal carcinoma (NPC) is a common tumor consistently associated with Epstein–Barr virus infection and prevalent in South China, including Hong Kong, and southeast Asia. Current genomic sequencing studies found only rare mutations in NPC, indicating its critical epigenetic etiology, while no epigenome exists for NPC as yet. Materials & methods: We profiled the methylomes of NPC cell lines and primary tumors, together with normal nasopharyngeal epithelial cells, using methylated DNA immunoprecipitation (MeDIP). Results: We observed extensive, genome-wide methylation of cellular genes. Epigenetic disruption of Wnt, MAPK, TGF-β and Hedgehog signaling pathways was detected. Methylation of Wnt signaling regulators (SFRP1, 2, 4 and 5, DACT2, DKK2 and DKK3) was frequently detected in tumor and nasal swab samples from NPC patients. Functional studies showed that these genes are bona fide tumor-suppressor genes for NPC. Conclusion: The NPC methylome shows a special high-degree CpG methylation epigenotype, similar to the Epstein–Barr virus-infected gastric cancer, indicating a critical epigenetic etiology for NPC pathogenesis.

Keywords::

• CpG methylation
• MeDIP
• methylome
• NPC
• tumor-suppressor gene
• WNT signaling

Financial & competing interests disclosure

This study was supported by the RGC (GRF#474710, TBRS#T12-401/13R) and the HMRF fund (#13120082) of Hong Kong and Research Schemes of The Chinese University of Hong Kong. The authors have no other relevant affiliations orfinancial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

No writing assistance was utilized in the production of this manuscript.

Ethical conduct of research

The authors state that they have obtained appropriate insti­tutional review board approval or have followed the princi­ples outlined in the Declaration of Helsinki for all human or animal experimental investigations. In addition, for investi­gations involving human subjects, informed consent has been obtained from the participants involved.

Additional information

Funding

This study was supported by the RGC (GRF#474710, TBRS#T12-401/13R) and the HMRF fund (#13120082) of Hong Kong and Research Schemes of The Chinese University of Hong Kong. The authors have no other relevant affiliations orfinancial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed. No writing assistance was utilized in the production of this manuscript.