The landscape of alternative splicing in cutaneous squamous cell carcinoma

Summary: Abstract Body: Dysregulation of RNA splicing is a feature in many cancers and has been implicated in cancer progression and therapeutic resistance. While alternative splicing events (ASE) have recently been reported in epidermal differentiation and skin homeostasis, little is known about the significance of ASE in cutaneous squamous cell carcinoma (cSCC). In this study, we sought to explore the landscape of ASE in cSCC compared to normal skin, identify candidate events that are associated with tumor progression, and validate the functional impacts of these occurrences. A cohort of 146 cSCC and 73 normal skin samples was investigated to determine ASE using rMATS-turbo. The initial comparison yielded 9,972 ASE (FDR<1%), including 2,535 skipped exon events. Further refinement of these 2,535 skipped exon events was conducted by imposing additional cutoffs for effect size and gene expression and retaining events with 1) opposite directionality in epidermal differentiation or 2) same directionality as observed in cSCC cell lines compared to differentiated keratinocytes. This approach yielded a list of 101 and 70 candidate events, respectively. Prominently, several genes functionally linked to cancer progression such as MAP3K7, EIF4A2, CD44 and FN1 showed alternative splicing in cSCC. Interestingly, exome analysis of 83 cSCC tumors revealed only rare splice site mutations in candidate genes and spliceosome-associated genes were not recurrently mutated in this cohort, suggesting other mechanisms are driving dysregulated splicing in cSCC. Efforts to validate these findings and determine the functional impact of cSCC-associated isoforms are currently underway. Their contribution to proliferation, invasion, and colony formation will provide a first indication of the overall importance of ASE in cSCC progression and novel pathways for cSCC treatment. Benjamin Genenger¹, Tomas Bencomo¹, Bryan Sun², Carolyn Lee^{1, 3} 1. Stanford Program in Epithelial Biology, Stanford University, Stanford, CA, United States. 2. Department of Dermatology, University of California Irvine, Irvine, CA, United States. 3. VA Palo Alto Health Care System, Palo Alto, CA, United States. UV Biology/Injury and Non-melanoma Cancers