Viral Integration Plays a Minor Role in the Development and Prognostication of Oral Squamous Cell Carcinoma

SIMPLE SUMMARY: Viruses are well known causes of several human malignancies. Oral squamous cell carcinoma (OSCC) is rising in patients with limited exposure to traditional risk factors, including smoking. As a causative factor of OSCC is yet to be found, our study aimed to identify a virus that may drive this cancer. First, we examined whole genome sequencing data from 28 patients under the age of 50 with limited exposure to carcinogens for viruses. Using viral detection software that screens for >700,000 viruses, we identified one 49 year old male patient with human papillomavirus (HPV). We further validated our findings in 657 patients, using immunohistochemistry and RNA in situ hybridization specific for HPV, and identified 8 (1.2%) male patients with HPV integration. Through a comprehensive search for viruses and evaluation in a large patient OSCC cohort, we demonstrate that viral integration occurs in a minority of male OSCC patients. ABSTRACT: Viruses are well known drivers of several human malignancies. A causative factor for oral cavity squamous cell carcinoma (OSCC) in patients with limited exposure to traditional risk factors, including tobacco use, is yet to be identified. Our study aimed to comprehensively evaluate the role of viral drivers in OSCC patients with low cumulative exposure to traditional risk factors. Patients under 50 years of age with OSCC, defined using strict anatomic criteria were selected for WGS. The WGS data was interrogated using viral detection tools (Kraken 2 and BLASTN), together examining >700,000 viruses. The findings were further verified using tissue microarrays of OSCC samples using both immunohistochemistry and RNA in situ hybridisation (ISH). 28 patients underwent WGS and comprehensive viral profiling. One 49-year-old male patient with OSCC of the hard palate demonstrated HPV35 integration. 657 cases of OSCC were then evaluated for the presence of HPV integration through immunohistochemistry for p16 and HPV RNA ISH. HPV integration was seen in 8 (1.2%) patients, all middle-aged men with predominant floor of mouth involvement. In summary, a wide-ranging interrogation of >700,000 viruses using OSCC WGS data showed HPV integration in a minority of male OSCC patients and did not carry any prognostic significance.