Gene expression profiling in HPV-infected oropharyngeal head and neck cancer

The prognosis of HPV-positive squamous oropharyngeal carcinomas (OPCs) is more favorable than that of HPV-negative OPCs. However, the prognosis of some of these tumors is dismal and to date validated survival predictors are missing in clinical practice. We designed a study on HPV-positive OPCs to determine whether a previously published gene expression tumor classification model,defined through meta-analysis of publicly available datasets (PMCID: PMC6721309), is able to predict survival in an external patient cohort. The 3 gene expression clusters were tested in a validation set of 286 cases and in a refined study population of 235 patients and in both confirmed their prognostic value. Five-year OS was 95% in the low risk cluster Cl1, 80% in the intermediate risk cluster (HR=5.74, p=.0057), and 66% in the high risk cluster (HR=9.28, p=.001). Functional/biological cluster characterization identified potentially targetable pathways in the high risk cluster. This prognostic stratification might be useful for clinical decision making and for planning future trials based on molecular tumor features. In our work, we considered a cohort of the HPV positive OPC patients included in the project “Big Data and Models for Personalized Head and Neck Cancer Decision Support (BD2Decide)”, trial registry ClinicalTrial.gov number NCT02832102. Patients were treated in seven European referral cancer centers (Italy, The Netherlands and Germany) with expertise in the multidisciplinary management of head and neck cancer patients. Median follow-up was 46.2 months (95% confidence interval 41.2-50) and data collection was concluded in September 2019 (doi:10.1002/hed.26515). OPC patients with loco-regionally advanced non-metastatic disease treated with curative intent were tested for HPV using p16-immunostaining and HPV DNA PCR and when positive included. HPV status was assessed by p16-immunostaining followed by a HPV DNA PCR test on the p16-immunopositive cases. Patients were treated with multimodal strategies (combinations of surgery, radiotherapy, and chemotherapy). For T1N1M0 and T2N1M0 disease single-modality treatment (surgery or radiotherapy) was allowed. To reduce the bias of confounding variables impacting on outcome, we excluded OPC: i) patients with p16-positive but HPV-DNA-negative OPC; ii) patients receiving unimodal treatment (surgery without post-operative radiation or exclusive radiotherapy without concomitant systemic treatments) for clinical stage T1N>1, T2N>1 and T3-T4 any N disease. TNM7= AJCC/UICC staging system 7th edition; TNM8= AJCC/UICC staging system 8th edition; subset (n=235)= exclusion of 51 HPV-DNA negative (n=14) OPCs and suboptimal treatments (n=37); HPV_molecular_clusters= gene-expression stratification based on Locati et al (PMCID: PMC6721309).