Frequently methylated tumor suppressor genes in head and neck squamous cell carcinoma

Cancer Res. 2008 Jun 15;68(12):4494-9. doi: 10.1158/0008-5472.CAN-07-6509.


Head and neck squamous cell carcinoma (HNSCC) is a very aggressive cancer. In advanced stages, the patient has poor chances of receiving effective treatment, and survival rates are low. To facilitate timely diagnosis and improve treatment, elucidation of early detection markers is crucial. DNA methylation markers are particularly advantageous because DNA methylation is an early event in tumorigenesis, and the epigenetic modification, 5-methylcytosine, is a stable mark. A genome-wide screen using Restriction Landmark Genomic Scanning found a set of genes that are most commonly methylated in head and neck cancers. Five candidate genes: septin 9 (SEPT9), sodium-coupled monocarboxylate transporter 1 (SLC5A8), functional smad-suppressing element on chromosome 18 (FUSSEL18), early B-cell factor 3 (EBF3), and iroquois homeobox 1 (IRX1) were methylated in 27% to 67% of the HNSCC patient samples tested. Furthermore, approximately 50% of the methylated tumor samples shared methylation between two of the five genes (most commonly between EBF3 and IRX1), and 15% shared methylation between three of the five genes. Expression analysis revealed candidate gene down-regulation in 25% to 93% of the HNSCC samples, and 5-aza-2'-deoxycytidine treatment was able to restore expression in at least 2 of 5 HNSCC cell lines for all of the genes tested. Overexpression of the three most frequently down-regulated candidates, SLC5A8, IRX1, and EBF3, validated their tumor suppressor potential by growth curve analysis and colony formation assay. Interestingly, all of the candidates identified may be involved in the transforming growth factor beta signaling pathway, which is often disrupted in HNSCC.

Publication types

  • Comparative Study
  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Azacitidine / pharmacology
  • Carcinoma, Squamous Cell / genetics*
  • Carcinoma, Squamous Cell / metabolism
  • Carcinoma, Squamous Cell / pathology
  • Cation Transport Proteins / genetics
  • Colony-Forming Units Assay
  • DNA Methylation*
  • Epigenesis, Genetic
  • GTP Phosphohydrolases / genetics
  • Gene Deletion
  • Gene Expression Regulation, Neoplastic
  • Genes, Tumor Suppressor / physiology*
  • Head and Neck Neoplasms / genetics*
  • Head and Neck Neoplasms / metabolism
  • Head and Neck Neoplasms / pathology
  • Homeodomain Proteins / genetics
  • Humans
  • Microtubule-Associated Proteins / genetics
  • Monocarboxylic Acid Transporters
  • Mucous Membrane / metabolism
  • Mucous Membrane / pathology
  • Nerve Tissue Proteins / genetics
  • Proto-Oncogene Proteins / genetics
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism
  • Reverse Transcriptase Polymerase Chain Reaction
  • Septins
  • Transcription Factors / genetics


  • Cation Transport Proteins
  • Homeodomain Proteins
  • IRX1 protein, human
  • MAPRE3 protein, human
  • Microtubule-Associated Proteins
  • Monocarboxylic Acid Transporters
  • Nerve Tissue Proteins
  • Proto-Oncogene Proteins
  • RNA, Messenger
  • SKOR2 protein, human
  • SLC5A8 protein, human
  • Transcription Factors
  • GTP Phosphohydrolases
  • SEPTIN9 protein, human
  • Septins
  • Azacitidine