Noncanonical HPV carcinogenesis drives radiosensitization of head and neck tumors

Abstract

We analyzed transcriptional data from 104 HPV+ (Human papillomavirus) HNSCC (head and neck squamous cell carcinoma) tumors together with two publicly available sources to identify highly robust transcriptional programs (modules) which could be detected consistently despite heterogeneous sequencing and quantification methodologies. Among 22 modules identified, we found a single module that naturally subclassifies HPV+ HNSCC tumors based on a bimodal pattern of gene expression, clusters all atypical features of HPV+ HNSCC biology into a single subclass, and predicts patient outcome in four independent cohorts. The subclass-defining gene set was strongly correlated with Nuclear factor kappa B (NF-κB) target expression. Tumors with high expression of this NF-κB module were rarely associated with activating PIK3CA alterations or viral integration, and also expressed higher levels of HPHPV E2 and had decreased APOBEC mutagenesis. Alternatively, they harbored inactivating alterations of key regulators of NF-κB, TNF receptor associated factor 3 (TRAF3), and cylindromatosis (CYLD), as well as retinoblastoma protein (RB1). HPV+ HNSCC cells in culture with experimental depletion of TRAF3 or CYLD displayed increased expression of the subclass-defining genes, as well as robust radio-sensitization, thus recapitulating both the tumor transcriptional state and improved treatment response observed in patient data. Across all gene sets investigated, methylation to expression correlations were the strongest for the subclass-defining, NF-κB-related genes. Increased tumor-infiltrating CD4+ T cells and increased Estrogen receptors alpha (ERα) expression were identified in NF-κB active tumors. Based on the relatively high rates of cure in HPV+ HNSCC, deintensification of therapy to reduce treatment-related morbidity is being studied at many institutions. Tumor subclassification based on oncogenic subtypes may help guide the selection of therapeutic intensity or modality for patients with HPV+ HNSCC.

De-Escalated Therapy and Early Treatment of Recurrences in HPV-Associated Head and Neck Cancer: The Potential for Biomarkers to Revolutionize Personalized Therapy

“…The association of HPV integration with outcome in head and neck tumors has had varied and conflicting results, with some studies showing no correlation with survival [ 54 , 62 ], some a positive correlation with viral integration [ 56 , 63 ], and others an unfavorable correlation [ 55 , 64 ]. Interestingly, to our knowledge, all studies using transcriptional (e.g., RNAseq) methods to ascertain integration status have found integration to be associated with poor prognosis [ 55 , 64 , 65 ]. A recent multiomics study of uterine cervical cancer categorized integration sites as productive or silent based on the presence or absence of viral-human fusion transcripts [ 66 ].…”

“…Testing the profile on four independent cohorts revealed that patients whose tumors had high expression of profile genes had significantly improved survival compared to those with low expression of these genes ( Table 1 ). Tumors assigned to the high expression vs. low expression subtypes were also distinguished by differences in somatic gene alterations, mutational signatures, HPV gene expression, HPV genome integration, and genomic methylation profiles [ 65 ]. The gene profile that identified the two subtypes of HPV+ HNSCC was based on high or low NF-κB signaling and fully recapitulated previous subtypes that our group defined based on the presence or absence of inactivating defects in TRAF3 or CYLD or associated gene expression changes [ 64 , 65 , 73 ].…”

“…Tumors assigned to the high expression vs. low expression subtypes were also distinguished by differences in somatic gene alterations, mutational signatures, HPV gene expression, HPV genome integration, and genomic methylation profiles [ 65 ]. The gene profile that identified the two subtypes of HPV+ HNSCC was based on high or low NF-κB signaling and fully recapitulated previous subtypes that our group defined based on the presence or absence of inactivating defects in TRAF3 or CYLD or associated gene expression changes [ 64 , 65 , 73 ]. Based on high vs. low expression of genes in the NF-κB signature, roughly 50% of patients were assigned to each subtype and previously reported molecular markers of good or poor prognosis appropriately sorted with the two subtypes; specifically, estrogen receptor-alpha expression [ 74 , 75 ] segregated with the subtype having high NF-κB activity and good survival, and PIK3CA defects segregated with the subtype having low NF-κB activity and poor survival.…”

“…On the other hand, tumors in the subtype with low NF-κB activity are radioresistant, implying that they will require a standard therapeutic dose or that they may be better suited for surgical or alternative therapies. The use of smoking history to identify patients for deintensified therapy is questionable given that it miscategorized smokers in the good, NF-κB high, prognosis group, and that smoking history was not correlated with diminished survival for this subtype [ 65 ].…”

Researchers identify two new subtypes of HPV‐associated head and neck cancers

“…In a study published in the Proceedings of the National Academy of Sciences, researchers used data from 104 HPV-related head and neck cancer tumors and other sources to identify gene expression patterns (or modules) from which different tumor types could be classified. 1 They found one module (of 22 identified) that was able to effectively categorize HPV-related head and neck tumors on the basis of a distinct gene expression pattern in which tumors were separated into high and low expression. Analysis of this module showed that the genes represented targets of a master transcription factor called nuclear factor-κB (NF-κB), a molecular pathway linked to cellular growth, formation of new blood vessels, and increased protection against cell death.…”