The Genome-Wide Molecular Landscape of HPV-Driven and HPV-Negative Head and Neck Squamous Cell Carcinoma

  • Farhoud Faraji
  • Adrian D. Schubert
  • Luciane T. Kagohara
  • Marietta Tan
  • Yanxun Xu
  • Munfarid Zaidi
  • Jean-Philippe Fortin
  • Carole Fakhry
  • Evgeny Izumchenko
  • Daria A. GaykalovaEmail author
  • Elana J. FertigEmail author
Part of the Current Cancer Research book series (CUCR)


Recent advances in sequencing technology have enabled unprecedented genome-wide characterization of head and neck squamous cell carcinoma (HNSCC). Integrated analyses of publicly available multiplatform high-throughput data have uncovered the vast genomic, epigenetic, and transcriptional diversity of HNSCC. Recognition of human papillomavirus (HPV) involvement in HNSCC carcinogenesis has resulted in the categorization of two HNSCC subtypes (HPV-driven and HPV-negative) with distinct etiologies, molecular properties, clinical features, and prognostic outcomes. Differences in the molecular landscapes of HPV-driven and HPV-negative HNSCC occur genome-wide and encompass changes in genomic, epigenetic, and transcriptional landscapes. Even within each subtype, HNSCC tumors have substantial inter-tumor and intra-tumor molecular heterogeneity. Improving the understanding of the underlying biological function of these complex molecular landscapes through emerging cross-platform genomic analyses is essential to developing more effective diagnostic and therapeutic strategies for HNSCC.


Head and neck squamous cell carcinoma Human papillomavirus Genomics Mutation Epigenetics Transcriptomics Heterogeneity Alternative splicing Gene fusion Immunotherapy 


Conflicts of Interest

The authors have no relevant conflicts of interest to declare.


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Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  • Farhoud Faraji
    • 1
  • Adrian D. Schubert
    • 1
  • Luciane T. Kagohara
    • 2
  • Marietta Tan
    • 1
  • Yanxun Xu
    • 3
  • Munfarid Zaidi
    • 1
  • Jean-Philippe Fortin
    • 4
  • Carole Fakhry
    • 1
  • Evgeny Izumchenko
    • 1
  • Daria A. Gaykalova
    • 1
    Email author
  • Elana J. Fertig
    • 2
    Email author
  1. 1.Department of Otolaryngology-Head and Neck SurgeryJohns Hopkins School of MedicineBaltimoreUSA
  2. 2.Department of Oncology and Division of Biostatistics and BioinformaticsSidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of MedicineBaltimoreUSA
  3. 3.Department of Applied Mathematics and StatisticsWhiting School of Engineering, Johns Hopkins UniversityBaltimoreUSA
  4. 4.Department of Biostatistics, Epidemiology, and InformaticsPerelman School of Medicine, University of PennsylvaniaPhiladelphiaUSA

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