Research Papers:

NF-κB over-activation portends improved outcomes in HPV-associated head and neck cancer

Travis P. Schrank, Andrew C. Prince, Tejas Sathe, Xiaowei Wang, Xinyi Liu, Damir T. Alzhanov, Barbara Burtness, Albert S. Baldwin, Wendell G. Yarbrough _ and Natalia Issaeva _

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Travis P. Schrank1,*, Andrew C. Prince1,*, Tejas Sathe2,3, Xiaowei Wang4,5, Xinyi Liu4,5, Damir T. Alzhanov1, Barbara Burtness6,9, Albert S. Baldwin6,9, Wendell G. Yarbrough1,7,8,# and Natalia Issaeva1,7,8,#

1 Department of Otolaryngology/Head and Neck Surgery, UNC, Chapel Hill, NC 27599, USA

2 Department of Surgery, Otolaryngology, Yale, New Haven, CT 06519, USA

3 Current address: Department of Surgery, Columbia University, New York, NY 10032, USA

4 Department of Pharmacology and Bioengineering, University of Illinois at Chicago, Chicago, IL 60612, USA

5 Bioinformatics Core, University of Illinois Cancer Center, Chicago, IL 60612, USA

6 Department of Medicine, Yale School of Medicine, New Haven, CT 06510, USA

7 Lineberger Cancer Center, UNC, Chapel Hill, NC 27599, USA

8 Department of Pathology and Laboratory Medicine, UNC, Chapel Hill, NC 27599, USA

9 Yale Cancer Center, Yale School of Medicine, New Haven, CT 06510, USA

* These authors contributed equally to this work

# Senior authors

Correspondence to:

Wendell G. Yarbrough, email: dell@med.unc.edu
Natalia Issaeva, email: natalia.isaeva@med.unc.edu

Keywords: HPV; head and neck cancer; CYLD; TRAF3; NF-κB

Received: March 23, 2022     Accepted: May 03, 2022     Published: May 24, 2022

Copyright: © 2022 Schrank et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.


Evolving understanding of head and neck squamous cell carcinoma (HNSCC) is leading to more specific diagnostic disease classifications. Among HNSCC caused by the human papilloma virus (HPV), tumors harboring defects in TRAF3 or CYLD are associated with improved clinical outcomes and maintenance of episomal HPV. TRAF3 and CYLD are negative regulators of NF-κB and inactivating mutations of either leads to NF-κB overactivity. Here, we developed and validated a gene expression classifier separating HPV+ HNSCCs based on NF-κB activity. As expected, the novel classifier is strongly enriched in NF-κB targets leading us to name it the NF-κB Activity Classifier (NAC). High NF-κB activity correlated with improved survival in two independent cohorts. Using NAC, tumors with high NF-κB activity but lacking defects in TRAF3 or CYLD were identified; thus, while TRAF3 or CYLD gene defects identify the majority of tumors with NF-κB activation, unknown mechanisms leading to NF-kB activity also exist. The NAC correctly classified the functional consequences of two novel CYLD missense mutations. Using a reporter assay, we tested these CYLD mutations revealing that their activity to inhibit NF-kB was equivalent to the wild-type protein. Future applications of the NF-κB Activity Classifier may be to identify HPV+ HNSCC patients with better or worse survival with implications for treatment strategies.

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