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

Abstract

The complex heterogeneity of head and neck squamous cell carcinoma (HNSCC) reflects a diverse underlying etiology. This heterogeneity is also apparent within Human Papillomavirus-positive (HPV+) HNSCC subtypes, which have distinct gene expression profiles and patient outcomes. One aggressive HPV+ HNSCC subtype is characterized by elevated expression of genes involved in keratinization, a process regulated by the oncogenic transcription factor ΔNp63. Furthermore, the human TP63 gene locus is a frequent HPV integration site and HPV oncoproteins drive ΔNp63 expression, suggesting an unexplored functional link between ΔNp63 and HPV+ HNSCC. Here we show that HPV+ HNSCCs can be molecularly stratified according to ΔNp63 expression levels and derive a ΔNp63-associated gene signature profile for such tumors. We leveraged RNA-seq data from p63 knockdown cells and ChIP-seq data for p63 and histone marks from two ΔNp63high HPV+ HNSCC cell lines to identify an epigenetically refined ΔNp63 cistrome. Our integrated analyses reveal crucial ΔNp63-bound super-enhancers likely to mediate HPV+ HNSCC subtype-specific gene expression that is anchored, in part, by the PI3K-mTOR pathway. These findings implicate ΔNp63 as a key regulator of essential oncogenic pathways in a subtype of HPV+ HNSCC that can be exploited as a biomarker for patient stratification and treatment choices.

Reciprocal inhibition between TP63 and STAT1 regulates anti-tumor immune response through interferon-γ signaling in squamous cancer

“…A negative correlation between the expression of TP63 and inflammatory/immune response-associated genes in HPV + HNSCC tumors was recently revealed using computational GO enrichment analysis 43 . Here we reveal a tumor-extrinsic role of TP63 in promoting immune evasion of SCC cells by suppressing the IFNγ-STAT1 signaling.…”

An integrated genomic approach identifies follistatin as a target of the p63-epidermal growth factor receptor oncogenic network in head and neck squamous cell carcinoma

“…Lentivirus-mediated depletion of p63 was performed using the pGIPZ system as previously described ( 29 ). pGIPZ lentiviral small hairpin RNA (shRNA#1; clone ID pV2LHS_201706; shRNA#2; clone ID pV2LHS_199988) targeting FST was obtained from gene modulation core facility at Roswell Park, Buffalo, NY.…”

“…HNSCC cells were processed for chromatin immunoprecipitation sequencing (ChIP-seq) experiments as previously described ( 29 ). Briefly, cells were grown to 80% confluency in 150-mm culture dishes and cross-linked with 1% formaldehyde for 10 min.…”

Potential Transcript-Based Biomarkers Predicting Clinical Outcomes of HPV-Positive Head and Neck Squamous Cell Carcinoma Patients

“…Whereas oncogenic viral integration favors overexpression of the TP63 gene conferring aggressive phenotypes such as keratinization and cell adhesion allowing tumor cell survival, either by direct or indirect repression of proapoptotic genes. Exploiting the value of viral site of integration as a biomarker could allow to stratify patients at risk and identify those who could benefit from certain treatments, such as EGFR and PI3K inhibitors, along with radiotherapy [64,65]. In summary, transcriptional data are useful to better detect HPV integration or HPV episome maintenance, which should be considered during the diagnosis and treatment of HPV-positive tumors due to the differential prognostic outcomes of patients [61,66].…”