Molecular Tumor Subtypes of HPV-Positive Head and Neck Cancers: Biological Characteristics and Implications for Clinical Outcomes

Abstract

Until recently, research on the molecular signatures of Human papillomavirus (HPV)-associated head and neck cancers mainly focused on their differences with respect to HPV-negative head and neck squamous cell carcinomas (HNSCCs). However, given the continuing high incidence level of HPV-related HNSCC, the time is ripe to characterize the heterogeneity that exists within these cancers. Here, we review research thus far on HPV-positive HNSCC molecular subtypes, and their relationship with clinical characteristics and HPV integration into the host genome. Different omics data including host transcriptomics and epigenomics, as well as HPV characteristics, can provide complementary viewpoints. Keratinization, mesenchymal differentiation, immune signatures, stromal cells and oxidoreductive processes all play important roles.

p63 Directs Subtype-Specific Gene Expression in HPV+ Head and Neck Squamous Cell Carcinoma

“…Segregation of HPV+ HNSCC tumors according to median p63 expression revealed distinct p63 high and p63 low subtypes. This distinction was in agreement with previous unsupervised gene expression clustering analyses performed on HPV+ HNSCC tumors that had identified subtypes with distinct gene expression patterns, including different p63 levels ( 11 , 14 , 51 ).…”

“…One notable finding is the wide range of p63 expression levels across the HPV+ tumors, which is clearly evident in several independent datasets. This reinforces results from previously defined subtypes of HPV+ HNSCC based on hierarchical clustering of gene expression ( 11 , 13 , 14 , 51 ). We provide evidence that the molecular and phenotypic attributes of the more aggressive p63 high HPV-KRT subtype, such as keratinization and cell adhesion, are likely controlled by a p63-driven direct transcriptional program.…”

“…A DAVID-based pathway analysis of the genes associated with the top 2,500 p63 ChIP-seq peaks revealed several important pathways, including those deemed important in HPV-associated cancers, such as focal adhesion, p53, and Rap1 signaling pathways ( Figure 2D ) ( 53 , 54 ). Interestingly, focal adhesion pathways are enriched in the subtype of HPV+ HNSCC tumors with high p63 expression levels ( 11 , 14 , 51 ). In parallel, we performed ChIP-seq of p63 in SCC152 utilizing the 4A4 antibody and identified 26,255 genomic peaks, with the p63 motif as the most enriched ( Supplementary Figures 3A, B and Supplementary Table 2 ).…”

“…The tumor microenvironment of HPV+ HNSCC is distinct from that of its HPV- counterpart, with greater immune infiltration, T-cell activation, and immunoregulation ( 51 ). Furthermore, two recent landmark single-cell-based studies indicated that HPV-specific infiltrating lymphocytes may mount an immune-based response to HPV+ HNSCC ( 78 , 79 ).…”

“…In these studies, HPV oncoprotein E2 was a target of particular interest, as E2 expression is often maintained in HPV+ HNSCC unlike in HPV+ cervical cancer. Interestingly, E2 expression is lower in the p63 high HPV-KRT subtype, most likely because of higher levels of HPV genomic integration, which disrupts HPV early gene expression ( 11 , 51 ). We suspect that the relatively lower immune cell infiltration and activation in HPV-KRT tumors may be attributable to their p63 high and E2 low state.…”