Squamous cell carcinomas (SCCs) and pre-malignant actinic keratoses (AKs) are thought to develop secondary to ultraviolet radiation (UV) damage. However, only ~10% of AKs progress and become SCCs. We use RNA NanoString nCounter® analysis to validate a novel, 80-gene ultraviolet radiation (UV)-associated biomarker panel for stratification of skin cancer risk. Based on our previous study, we selected 80 of the 125 highly conserved UV-responsive genes to validate for clinical utility as a biomarker panel for detecting cancer-prone skin lesions. We enrolled patients with clinically evident AKs adjacent to NS or cutaneous SCCs adjacent to NS undergoing Mohs micrographic surgery (MMS). Diagnosis was confirmed histopathologically. RNA was isolated and NanoString nCounter® flex system was used on matched samples to quantify expression of the 80 biomarker genes. Dendrogram and supervised hierarchical clustering heat map of SCCs and AKs based on differential expression of the selected UV biomarker genes between each AK/SCC and their respective NS pair. Dot plots were created highlighting differential expression of selected biomarker genes for each AK/SCC and their respective NS pair based on fold-change. Results identified 33/80 selected UV responsive genes as consistently dysregulated in more than 50% of human primary SCC samples. Results showed hierarchical clustering of SCCs into two subgroups, with one more strongly corroborated with the UV signature. The AKs form a distinctive cluster showing an intermediate level of UV biomarker gene expression, except two outliers. The genes selected for this UV-biomarker panel corroborate the theory that AKs exist on a continuum with SCCs and their UV gene signature may allow for better risk stratification. The finding of two SCC subgroups also suggests that there may be two different major molecular pathways, one of which is more highly UV-dependent, underpinning SCC pathogenesis.

Development and Validation of an 80-Gene UV Biomarker Panel for Stratification of Skin Cancer Risk