Abstract 815: Integrated genomic analysis of cutaneous squamous cell carcinoma progression.
Authors: Chitsazzadeh Vida , Xiao Weimin , Gunaratne Preethi , Coarfa Cristian , Su Xiaoping , Nguyen Tri H. , Thomas Valencia D. , Joseph Aaron K. , Flores Elsa R. , Tsai Kenneth Y. 
Published: August 2014

Abstract
Skin cancer is the most common class of malignancy in humans. In the United States, there are over 3 million cases of skin cancer a year with significant costs not only in morbidity and mortality, but an estimated $500 million in treatment-related costs and $2 billion in overall economic impact including lost productivity. The vast majority of these skin cancers arise in keratinocytes and within this group, cutaneous squamous cell carcinoma (cSCC) comprises 15-20% of cases. cSCC has the best-defined progression from a distinct precancerous lesion, the actinic keratosis (AK) to invasive cSCC which has appreciable metastatic potential particularly in high-risk scenarios. Beyond serial, disfiguring surgeries, there is no effective therapy.
AKs are the most common precancerous lesion in humans, affecting upwards of 5.5% of women and 13.9% of men in U.S. Our understanding of the molecular events that lead from normal skin to AK to cSCC is very poor and represents a fundamental gap in our understanding of this progression sequence. Such an understanding would be of enormous importance. While destructive modalities are the mainstay of treatment of AK, they must be repetitively used and there is no basis for identifying those most likely to progress. Therefore, there is a tremendous need for rationally designed targeted diagnostics and therapy for AKs, which presents an ideal opportunity for molecularly-informed skin cancer screening and secondary prevention.
We have performed next generation sequencing (Illumina HiSeq) for microRNA and mRNA on matched samples from 10 patients. Each matched set is composed of clinically normal skin, AK, and cSCC from the same patient, minimizing background genetic heterogeneity. For miRNA-seq, 6.1 million reads with 720,000 mapped reads were obtained on average. RNA-seq analysis yielded over 64 million reads per sample with 92% mapped. Following unsupervised clustering, we found cSCCs clustered together, and AKs clustered with both normal skin and with cSCC confirming the clinico-pathologic characterization of these lesions as precursors to cSCC.
Changes in expression of only two miRNA and 367 mRNA emerged as the most significant predictors of overall progression from normal skin to AK to cSCC. In pairwise comparisons between normal skin and cSCC, we identified 628 functional miRNA-mRNA pairs comprising a total of 59 miRNA and 179 predicted mRNA targets. Surprisingly, the number of miRNA and mRNA expression changes between AK and cSCC were very limited (&lt;50 mRNA and &lt;10 miRNA). These findings are in stark contrast to many previously reported studies on un-matched samples, which validates our novel approach. We are functionally validating our findings in cells and in our mouse model of UV-driven SCC, and we anticipate that we will identify key drivers of cSCC progression that will yield insights relevant for other cancers.
Citation Format: Vida Chitsazzadeh, Weimin Xiao, Preethi Gunaratne, Cristian Coarfa, Xiaoping Su, Tri H. Nguyen, Valencia D. Thomas, Aaron K. Joseph, Elsa R. Flores, Kenneth Y. Tsai. Integrated genomic analysis of cutaneous squamous cell carcinoma progression. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 815. doi:10.1158/1538-7445.AM2013-815