A proteomic signature associated with prognosis in HPV-related locally advanced oropharyngeal squamous cell carcinoma (LA-OPSCC).

Abstract

6055 Background: Although HPV-related LA-OPSCC is associated with better prognosis than HPV-negative disease, ~30% of cases relapse despite curative-intent chemoradiotherapy. New prognostic biomarkers are needed to rationalise curative-intent treatment without compromising efficacy. We aimed to develop a proteomic signature associated with risk of recurrence from diagnostic biopsies of patients with HPV-positive OPSCC. Methods: We analysed 139 formalin fixed paraffin embedded archival core biopsy specimens from 124 patients with HPV-related (p16 IHC positive) T1-4N0-3M0 LA-OPSCC tumours. All patients were treated with definitive chemoradiotherapy at the Princess Alexandra Hospital (Brisbane, Australia) between 2007-2019. The cohort included 50 patients with recurrence less than five years from diagnosis and 74 age/performance-status matched patients with no recurrence. Proteomic analysis was performed utilizing data-independent acquisition mass spectrometry (DIA-MS). A proteomic prognostic signature associated with recurrence free survival (RFS) at five years was the primary endpoint of interest. It was developed using a computational pipeline comprising an initial univariate Cox model step, followed by multiple runs of multivariate Cox models with Least Absolute Shrinkage and Selection Operator (LASSO) regularization, and then a final step of recursive feature selection. Results: A total of 7,597 proteins were quantified and 665 were differentially expressed proteins between tumour and normal adjacent tissues. There were 5,199 proteins remaining in the tumour samples after filtering. RFS was significantly (q-value < 0.05) associated with 252 proteins, whose functions are enriched in adaptive and innate immunity and MAPK6/MAPK4 signalling pathways. A 16-protein signature associated with RFS stratified patients into low, intermediate, or high-risk groups (C-index = 0.885, p < 0.0001). The 16-protein signature outperformed clinico-pathological covariates including age, stage, ECOG and smoking history with the highest area under the receiver operating characteristic curve (AUROC 0.95). Conclusions: DIA-MS-based proteomics on core biopsies can be used to risk stratify HPV-related OPSCC patients. A 16-protein signature associated with RFS was successfully identified as a basis for future studies. Validation of this proteomic prognostic signature in independent cohorts is required and may be used to inform future clinical trials to better tailor upfront therapy.