Development of a Clinical Assay to Guide Patient Therapy in HPV-Associated Head and Neck Cancer

Purpose: Patients with human papillomavirus–associated head and neck squamous cell carcinoma (HPV+ HNSCC) have relatively favorable outcomes, but standard treatments like radiation or chemoradiation frequently result in long-term toxic side effects. Appropriate patient selection has been a barrier to effectively de-escalate therapy for HPV+ HNSCC, and the absence of accurate biomarkers likely contributed to failure of recent promising de-escalation trials that rely on histologic tumor characteristics, history of tobacco use, or tumor response to chemotherapy; This deficiency underlines the need to develop and validate an assay to accurately detect two subtypes of HPV+ HNSCC—one with good prognosis and one with poor prognosis. Experimental Design: These two subtypes are distinguished by the activity of NF-κB in tumors. We first developed a DNA-based marker panel consisting of genes that when mutated would lead to NF-κB activation. Additionally, we developed a custom NanoString assay to determine the expression of NF-κB target genes. These assays were tested to determine their accuracy in detecting tumor subtype. Results: We demonstrate that the NF-κB gene signature score, as determined using the NanoString assay, could more accurately classify HPV+ HNSCC as compared with the DNA-based marker panel. Patients with a high NF-κB gene signature score demonstrated significantly increased overall survival, indicating more sensitivity to (chemo)radiation treatment. Conclusions: The NF-κB gene signature score can accurately predict response to standard (chemo)radiation in HPV+ HNSCC. This molecular biomarker holds promise for clinical use in identifying patients who are likely to benefit from treatment deescalation strategies, potentially reducing long-term side effects without compromising therapeutic efficacy.