A Systemic and Integrated Analysis of p63-Driven Regulatory Networks in Mouse Oral Squamous Cell Carcinoma

SIMPLE SUMMARY: Oral squamous cell carcinomas (OSCC) are the most common malignancies affecting the oral cavity and account for 40% of all head and neck squamous cell carcinoma cases. Unfortunately, patient outcomes are generally unfavorable, as diagnosis normally occurs at a late stage of the disease, as well as a lack of effective targeted treatments. Our identification of potential prognostic biomarkers is of particular importance to the field and could lead to the generation of effective targeted therapies which may improve patient outcomes and survival. Here, we utilize a mouse model of OSCC to explore the role of p63 as an important oncogenic transcription factor in the control of OSCC proliferation and migration. We also generate a p63-driven gene expression signature for mouse OSCC which identifies both novel and conserved genes and pathways, which may be relevant in human disease and which may serve as potential biomarkers and targets for future therapeutics. ABSTRACT: Oral squamous cell carcinoma (OSCC) is the most common malignancy of the oral cavity and is linked to tobacco exposure, alcohol consumption, and human papillomavirus infection. Despite therapeutic advances, a lack of molecular understanding of disease etiology, and delayed diagnoses continue to negatively affect survival. The identification of oncogenic drivers and prognostic biomarkers by leveraging bulk and single-cell RNA-sequencing datasets of OSCC can lead to more targeted therapies and improved patient outcomes. However, the generation, analysis, and continued utilization of additional genetic and genomic tools are warranted. Tobacco-induced OSCC can be modeled in mice via 4-nitroquinoline 1-oxide (4NQO), which generates a spectrum of neoplastic lesions mimicking human OSCC and upregulates the oncogenic master transcription factor p63. Here, we molecularly characterized established mouse 4NQO treatment-derived OSCC cell lines and utilized RNA and chromatin immunoprecipitation-sequencing to uncover the global p63 gene regulatory and signaling network. We integrated our p63 datasets with published bulk and single-cell RNA-sequencing of mouse 4NQO-treated tongue and esophageal tumors, respectively, to generate a p63-driven gene signature that sheds new light on the role of p63 in murine OSCC. Our analyses reveal known and novel players, such as COTL1, that are regulated by p63 and influence various oncogenic processes, including metastasis. The identification of new sets of potential biomarkers and pathways, some of which are functionally conserved in human OSCC and can prognosticate patient survival, offers new avenues for future mechanistic studies.