Skip to main content
An official website of the United States government

Head and Neck Squamous Cell Carcinoma Study

What are head and neck cancers?

Most head and neck cancers begin in the moist, mucus membranes lining the inside of the mouth, nose and throat. These membranes are made up of squamous cells and the head and neck cancers that grow in these cells are called squamous cell carcinomas.

These cancers most often affect people over the age of 50 and the rates in men are more than twice as high as the rates in women.1 In 2010, about 36,000 Americans are estimated to have been diagnosed with head and neck cancers and an estimated 7,880 were expected have died of squamous cell carcinomas. Known risks for developing head and neck cancers are smoking and heavy drinking. Additional information on head and neck cancers.

What have TCGA researchers learned about head and neck cancers?

  • Head and neck cancers associated with human papillomavirus (HPV) and tobacco-smoking are molecularly distinct.
    • The integration of HPV, a virus harboring oncoproteins E6 and E7 that cause HPV positive head and neck squamous cell carcinomas, is linked to increased somatic copy number variants.
    • HPV-positive tumors are also characterized by:
      • Shortened or deleted TRAF3, a gene that codes for a protein that helps regulate the body’s immune response
      • Amplification of E2F1, a gene encoding a member of the E2F transcription factor family that is involved in cell cycle regulation
      • Mutations in PIK3CA
    • HPV-negative tumors contained novel co-amplifications of 11q13 and 11q22, an event that likely promotes the interaction of BIRC2 and FADD, genes that together work to inhibit cell death.
    • Smoking-related tumors featured TP53 mutations, CDKN2A inactivation, and frequent copy number alterations.
  • Molecular characteristics may help clinicians improve the specificity of the diagnosis and treatment of head and neck squamous cell carcinomas.
    • Cell cycle proteins are altered in differently in HPV-positive and HPV-negative cancers, suggesting that treating these cancers should be treated according to their subtype.