UV biomarker genes for classification and risk stratification of cutaneous actinic keratoses and squamous cell carcinoma subtypes

Dawn Queen, Yao Shen, Megan H. Trager, Adriana T. Lopez, Faramarz H. Samie, Jesse M. Lewin, George W. Niedt, Larisa J. Geskin, Liang Liu

Research output: Contribution to journalArticlepeer-review


Currently, there is no sensitive molecular test for identifying transformation-prone actinic keratoses (AKs) and aggressive squamous cell carcinoma (SCC) subtypes. Biomarker-based molecular testing represents a promising tool for risk stratifying these lesions. We evaluated the utility of a panel of ultraviolet (UV) radiation-biomarker genes in distinguishing between benign and transformation-prone AKs and SCCs. The expression of the UV-biomarker genes in 31 SCC and normal skin (NS) pairs and 10 AK/NS pairs was quantified using the NanoString nCounter system. Biomarker testing models were built using logistic regression models with leave-one-out cross validation in the training set. The best model to classify AKs versus SCCs (area under curve (AUC) 0.814, precision score 0.833, recall 0.714) was constructed using a top-ranked set of 13 UV-biomarker genes. Another model based on a 15-gene panel was developed to differentiate histologically concerning from less concerning SCCs (AUC 1, precision score 1, recall 0.714). Finally, 12 of the UV-biomarker genes were differentially expressed between AKs and SCCs, while 10 genes were uniquely expressed in the more concerning SCCs. UV-biomarker gene subsets demonstrate dynamic utility as molecular tools to classify and risk stratify AK and SCC lesions, which will complement histopathologic diagnosis to guide treatment of high-risk patients.

Original languageEnglish (US)
Pages (from-to)13022-13032
Number of pages11
JournalFASEB Journal
Issue number9
StatePublished - Sep 1 2020

Bibliographical note

Funding Information:
Funding through NIH/NIAMS grant K01AR064315; the Prevent Cancer Foundation research award; the Columbia University Herbert Irving Comprehensive Cancer Center (P30 CA013696)

Publisher Copyright:
© 2020 Federation of American Societies for Experimental Biology


  • actinic keratosis
  • squamous cell carcinoma
  • ultraviolet radiation

PubMed: MeSH publication types

  • Journal Article
  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't


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