The Impact Of Intratumoral Heterogeneity Parameters On Prognosis In Head And Neck Squamous Cell Carcinoma

Head and Neck cancer (HNC) affects approx. 65,000 people in the US alone, representing an important healthcare burden. While certain prognostic factors such as HPV status has been previously established in a subset of H&N tumors, considerable outcome differences exist among HPV positive and negative patients, suggesting the need for further refinement of prognostic molecular markers. Intra-tumoral heterogeneity (ITH) has been previously associated with survival in HNC, but data for the impact of anatomic location on intra-tumoral heterogeneity are poorly understood. In this analysis, we included several parameters representing established metrics of intratumoral heterogeneity in 445 primary head and neck tumors from individual patients compiled in The Cancer Genome Atlas and published previously with follow-up data. We evaluated mutation burden, number of clones, Shannon index with increasing values representing greater intratumoral heterogeneity, subclone prevalence, major clone proportion determined by whole-exome or whole genome sequencing. Anatomic subsites included 105 larynx (10 tumors representing hypopharynx), 159 oral cavity (excluding oral tongue), 111 oral tongue and 60 oropharyngeal samples. Analysis was carried out using Cox-proportional hazard ratio and log-rank test using two-sided. The impact of individual ITH metrics varied vastly between anatomic locations. In oral tongue tumors, mutational burden was the only metric significantly associated with worse prognosis after adjustment for age at diagnosis (HR 1.08-5.8, p = 0.002.) In oral cavity tumors, age at diagnosis represented an independent prognostic parameter (HR 1.01-1.1, p = 0.003) and no ITH metric remained independently predictive after adjustment for age at diagnosis. The overall survival of oropharyngeal patients was significantly worse in those with high PyClone-derived Shannon Index in which increasing value correlates with increased ITH (p = 0.04) after adjustment for age at diagnosis and mutation burden. Laryngeal tumors had the highest mean (669.79 vs. 261.3 in tongue SCC) and median (451 vs. 228 in tongue SCC) mutation burden, yet no ITH parameter was independently associated with overall prognosis. This analysis demonstrates that intratumoral heterogeneity in HNC represents a potentially meaningful biomarker when applied with consideration of individual anatomic subsite and in combination with other prognostic parameters. While limited by the absence of full clinical data such as stage or treatment received, pending prospective validation, it may prove useful to guide future treatment decisions and clinical trial designs.