104 Lack of human papilloma virus transcription in cutaneous squamous cell carcinoma stratified by histological grade and host immune status

Human Papilloma Virus (HPV) infection is known to contribute to mucosal (m)SCC, but its role in cutaneous (c)SCC progression remains unclear, especially in lesions determined to be at high-risk for metastasis. We hypothesized that histologically high grade cSCCs in immunosuppressed patients would display increased transcriptional activity of HPV when compared to low histologic grade lesions in otherwise healthy patients. To assess the role of viruses in cSCC pathogenesis we utilized high throughput RNA sequencing across risk-stratified lesions. A total of 22 skin excisions (11 classified as high grade in immunocompromised patients, 8 classified as low grade in otherwise healthy patients, and 3 as normal skin) were used for detection of any non-human RNA. Reads were aligned to known viral transcriptomes using our recently developed Microbiome Coverage Profiler. While approximately two-thirds of all samples tested positive for HPV gDNA, no skin sample had detectable expression of HPV RNA. Instead, many were found to have expression of Human Endogenous Retroviruses, Simian Virus 40, and Staphylococcus Prophages, while analysis of published datasets of sequenced HeLa cells demonstrated numerous RNA reads for HPV. These results suggest that either HPV does not participate in cSCC development, or facilitates cSCC initiation without effecting tumor progression. The ability to monitor viral and prophage gene expression in skin biopsies will provide insights into the interplay of host-pathogen interactions, and the framework described herein can be used to analyze skin biopsies to facilitate understanding in cases where pathogens are thought to contribute to disease pathogenesis.