RAB25 expression is epigenetically downregulated in oral and oropharyngeal squamous cell carcinoma with lymph node metastasis

M. J. A. M. Clausen, L. J. Melchers, M. F. Mastik, L. Slagter-Menkema, H. J. M. Groen, B. F. A. M. van der Laan, W. van Criekinge, T. de Meyer, S. Denil, B. van der Vegt, G. B. A. Wisman, J. L. N. Roodenburg, E. Schuuring*

*Corresponding author for this work

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Abstract

Oral and oropharyngeal squamous cell carcinoma (OOSCC) have a low survival rate, mainly due to metastasis to the regional lymph nodes. For optimal treatment of these metastases, a neck dissection is required; however, inaccurate detection methods results in under- and over-treatment. New DNA prognostic methylation biomarkers might improve lymph node metastases detection. To identify epigenetically regulated genes associated with lymph node metastases, genome-wide methylation analysis was performed on 6 OOSCC with (pN+) and 6 OOSCC without (pN0) lymph node metastases and combined with a gene expression signature predictive for pN+ status in OOSCC. Selected genes were validated using an independent OOSCC cohort by immunohistochemistry and pyrosequencing, and on data retrieved from The Cancer Genome Atlas. A two-step statistical selection of differentially methylated sequences revealed 14 genes with increased methylation status and mRNA downregulation in pN+ OOSCC. RAB25, a known tumor suppressor gene, was the highest-ranking gene in the discovery set. In the validation sets, both RAB25 mRNA (P = 0.015) and protein levels (P = 0.012) were lower in pN+ OOSCC. RAB25 mRNA levels were negatively correlated with RAB25 methylation levels (P <0.001) but RAB25 protein expression was not. Our data revealed that promoter methylation is a mechanism resulting in downregulation of RAB25 expression in pN+ OOSCC and decreased expression is associated with lymph node metastasis. Detection of RAB25 methylation might contribute to lymph node metastasis diagnosis and serve as a potential new therapeutic target in OOSCC.

Original languageEnglish
Pages (from-to)653-663
Number of pages11
JournalEpigenetics
Volume11
Issue number9
DOIs
Publication statusPublished - 2016

Keywords

  • DNA methylation
  • epigenetic regulation
  • head and neck cancer
  • metastasis
  • MethylCap-Seq
  • oral squamous cell carcinoma
  • NECK-CANCER
  • DIFFERENTIAL EXPRESSION
  • PROMOTER METHYLATION
  • BREAST-CANCER
  • HEAD
  • GENE
  • IDENTIFICATION
  • VALIDATION
  • MICROARRAY
  • PREDICTION

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