Gene expression landscape of cutaneous squamous cell carcinoma progression

Abstract

BackgroundCutaneous squamous cell carcinomas (SCC) are the second most common human cancer and have been characterized by RNA sequencing (RNA-Seq); however, the transferability of findings from individual studies may be limited by small sample sizes and diverse analysis protocols. ObjectivesTo define the transcriptome landscape at different stages in the progression of normal skin to SCC through a meta-analysis of publicly available RNA-Seq samples MethodsWhole-transcriptome data from 73 normal skin samples, 46 actinic keratoses (AK), 16 in situ SCC, 13 keratoacanthomas (KA), and 147 SCC (including 30 SCC from immunocompromised patients and 8 SCC from individuals with recessive dystrophic epidermolysis bullosa [RDEB]) was uniformly processed to harmonize gene expression. Differential expression, fusion detection, and cell-type deconvolution analyses were performed. ResultsIndividual RNA-Seq studies of SCC demonstrated study-specific clustering and varied widely in their differential gene expression detection. Following batch correction, we defined a consensus set of differentially expressed genes (DEGs), including those altered in the preinvasive stages of SCC development, and used single-cell RNA-Seq data to demonstrate that DEGs are often, but not always, expressed by tumor-specific keratinocytes (TSKs). Analysis of the cellular composition of SCC, KA, and RDEB-SCC identified an increase in differentiated keratinocytes in KA, while RDEB-SCC contained the most TSKs. Compared to SCC arising in immunocompetent patients, SCC from immunosuppressed individuals demonstrated fewer memory B cells and CD8 T cells. A comprehensive and unbiased search for fusion transcripts in SCC and intermediate disease stages identified few candidates that recur in >1% of all specimens, suggesting most SCC are not driven by oncogenic gene fusions. Finally, using GTEx data, we distilled a novel 300-gene signature of chronic sun exposure that affirms greater cumulative ultraviolet (UV) exposure in later stages of SCC development. ConclusionsOur results define the gene expression landscape of SCC progression, characterize cell subpopulation heterogeneity in SCC subtypes that contribute to their distinct clinical phenotypes, demonstrate that gene fusions are not a common cause of SCC, and identify UV-responsive genes associated with SCC development. What is already known about this topic?O_LICutaneous squamous cell carcinoma (SCC) is one of the most common cancers worldwide. C_LIO_LISeveral studies have examined gene expression changes in SCC using RNA sequencing (RNA-Seq) but comparison of their results is difficult due to inter-study variation and diverse bioinformatic pipelines and protocols. C_LIO_LIA few gene fusions have been described in SCC, but a comprehensive characterization of fusion transcripts in patient samples has not been performed. C_LI What does this study add?O_LIWe re-analyzed RNA-Seq data from 11 studies of SCC and its preinvasive stages to create a list of consensus differentially expressed genes and identify those that are UV-responsive. C_LIO_LIClinically aggressive SCC displayed more tumor-specific keratinocytes, while keratoacanthomas contained more differentiated keratinocytes. SCC in immunocompetent persons had more memory B cells and CD8 T cells than those arising in immunosuppressed individuals. C_LIO_LIPreviously reported gene fusions were not detected and most fusion candidates did not demonstrate pathogenic features. C_LI What is the translational message?O_LIOur analysis harmonizes differing results from previous studies to provide a robust list of genes implicated in SCC development. C_LIO_LIOur findings suggest gene fusions are not a common driver event in SCC. C_LI