Molecular correlates for HPV-negative head and neck cancer engraftment prognosticate patient outcomes

There is a pressing need to improve risk stratification and treatment selection for HPV-negative head and neck squamous cell carcinoma (HNSCC) due to the adverse side effects of treatment. One of the most important prognostic features is metastases in lymph nodes. Previously, we demonstrated that tumor formation in patient-derived xenografts (i.e. engraftment) was associated with poor clinical outcomes in patients with HPV-negative HNSCC. However, assessing engraftment is challenging to implement in clinical settings. Here, we performed transcriptomic and proteomic profiling of 88 HNSCC patients and found the relationship between engraftment and clinical outcomes was recapitulated by molecular phenotype. We identified LAMC2 and TGM3 as candidate prognostic biomarkers and validated their utility in an independent cohort containing 404 HPV-negative HNSCC patients. Strikingly, these markers significantly improve prediction of outcomes beyond nodal status alone and can significantly stratify patients without any nodal involvement. Overall, our study demonstrates how the molecular characteristics of engraftment can inform patient prognostication. Overall design: RNA-seq of Cal33 and Cal27 tongue squamous cell carcinoma cells and 61137 and 61162 carcinoma-associated fibroblast cells in mono-culture or co-culture.