Lack of human papilloma virus transcriptional activity 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. Skin excisions classified as high grade in immunocompromised patients, low grade in otherwise healthy patients, and 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. To assess the role of HPV and other viral gene expression in cSCC disease pathogenesis we have utilized high throughput sequencing of cSCC across risk-stratified lesions. A collection of histologically high-risk, low-risk, and normal skin biopsies were used for detection of non-human RNA. High-quality, non-human reads were used for viral analysis using Microbiome Coverage Profiler and differential human gene expression analysis were conducted comparing risk groups to normal skin using edgeR. The processed data for these records includes only the differential human gene expression analysis. The HPV DNA Detection status of these samples was not available at the time of submission but submitter states that the records will be updated with this information when it becomes available.