Abstract 3491: Tumor subtype classification of HPV-associated head and neck cancers is central to key clinically relevant variables
Authors: Garb Bailey F. , Li Shiting , Qin Tingting , Lopez Elizabeth , Soppe Sarah , Patil Snehal , Rozek Laura , D'Silva Nisha , Sartor Maureen 
Published: March 2024

Abstract
Cancer types are typically categorized according to the cell of origin, but within these groupings there exists vast heterogeneity. Thus, subtypes based on molecular features are often defined that have clinical utility as prognostic biomarkers, aid in selection of therapeutic strategies, or are associated with treatment response. Head and neck cancer (HNC) is the seventh most common cancer globally and projected to have 54,540 new cases in the U.S. in 2023. Within the US, HPV(+) HNC is now more prevalent than HPV(+) cervical cancer, and it is expected to continue to rise. Although there is wide morphologic and epigenetic diversity within HPV(+) HNC, tumor subtyping is not yet widely used for this cancer population, largely because of HPV(+) HNC’s unique tumorigenesis process. Unlike other cancers that are driven by specific genetic signatures, HNC is driven by viral gene mechanisms. Given the large degree of heterogeneity among HPV(+) HNC cases and the lack of key mutations to define subtypes, the classification of HPV(+) HNSC subtypes requires a more sophisticated approach.
In this study, we introduce a robust, ensemble machine learning (ML) classifier for subtyping HPV(+) HNC that was trained on multiple cohorts and gene feature sets from RNA-seq data, and rigorously tested to ensure high reproducibility. The results classify HPV(+) HNC into the two main recognized subtypes: IMU (immune strong) and KRT(highly keratinized). Using a cohort of 227 patients, we show that the IMU/KRT classification is highly correlated with key clinically relevant variables in HNC. Of 41 molecular, clinical, and epidemiologic variables tested, 24 significantly associated with subtype. The IMU subtype was significantly associated with CD8 T-cells (p-value = 4.21 × 10−9), Dendritic cells (p-value = 1.65 × 10−8), B-cells (p-value = 2.20E−8), and epithelial to mesenchymal transition (p-value = 0.00013146). The KRT subtype is significantly associated with keratinization (p-value = 7.11 × 10−9), HPV integration (p-value = 3.14 × 10−6), radiation resistance (p-value = 0.00307), female sex (p-value = 0.00641), and high T stage (p-value = 0.0324). Genetic, epigenetic, and HPV gene-related variables were also among those significantly associated with subtype.
HPV(+) HNC subtypes have been shown to be associated with survival, with KRT-like patients having worse clinical outcomes than IMU. Given the different carcinogenic processes underlying IMU and KRT tumors, our ensemble ML subtype classifier web tool will help inform future studies of HPV(+) HNC. Future work to assess how HPV(+) subtypes can be incorporated into precision treatment strategies is well-motivated by our findings.
Citation Format: Bailey F. Garb, Shiting Li, Tingting Qin, Elizabeth Lopez, Sarah Soppe, Snehal Patil, Laura Rozek, Nisha D'Silva, Maureen Sartor. Tumor subtype classification of HPV-associated head and neck cancers is central to key clinically relevant variables [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3491.