Outcomes Stratification of Head and Neck Cancer Using Pre- and Post-Treatment DNA Methylation in Peripheral Blood

Purpose/objective(s) Established risk factors for head and neck cancer recurrence include clinical and tumor features assessed prior to treatment. We report the first use of DNA methylation in peripheral blood before and after radiotherapy (RT) to further improve risk stratification. Materials/methods Peripheral blood samples were obtained from patients with non-metastatic squamous cell carcinoma (SCC) of the head and neck for methylation analysis, 1 week before initiation and 1 month after completion of RT. Patients were randomized to a discovery cohort or validation cohort. In the discovery cohort, associations between methylation change at 807,100 genomic sites (post-treatment minus pre-treatment) and progression-free survival (PFS) as well as overall survival (OS) were evaluated using Cox regression, adjusted for clinicopathologic covariates. A risk score (RS) was then constructed from methylation levels at the top associated sites, filtered for residing within regulatory elements of genes that are predominantly expressed in bone marrow, lymphoid tissue, or blood cells. The prognostic value of RS was separately assessed in the discovery cohort and validation cohort. Results Between December 2013 and September 2018, 115 patients enrolled in this study (Table) and consist of mostly males (72%) with locally advanced disease (91%). HPV negative status, oral cavity cancer, PEG tube insertion, and higher neutrophil count before RT were associated with shorter PFS and OS (P 10, P = 0.016) and OS (HR > 10, P = 0.017) in the discovery cohort, independent of the aforementioned risk factors. These findings were further replicated in the validation cohort where high RS also independently conferred poorer PFS (HR > 10, P = 0.002) and OS (HR 6.3, P = 0.015). Conclusion We successfully trained and validated a signature of DNA methylation in peripheral blood before and after RT that stratified outcomes among patients with head and neck SCC, implicating the potential for genomics-tailored consolidation treatment and surveillance. Efforts toward methylation analysis at additional post-treatment time points are ongoing.