Key differences identified between actinic keratosis and cutaneous squamous cell carcinoma by transcriptome profiling

Abstract

Background: Cutaneous squamous cell carcinoma (cSCC) is one of the most common malignancies in fair-skinned populations worldwide and its incidence is increasing. Despite previous observations of multiple genetic abnormalities in cSCC, the oncogenic process remains elusive. The purpose of this study was to elucidate key molecular events associated with progression from premalignant actinic keratoses (AKs) to invasive cSCC by transcriptome profiling.

Methods: We combined laser capture microdissection with the Affymetrix HGU133 Plus 2.0 microarrays to profile 30 cSCC and 10 AKs.

Results: We identified a core set of 196 genes that are differentially expressed between AK and cSCC, and are enriched for processes including epidermal differentiation, cell migration, cell-cycle regulation and metabolism. Gene set enrichment analysis highlighted a key role for the mitogen activated protein kinase (MAPK) pathway in cSCC compared with AK. Furthermore, the histological subtype of the tumour was shown to influence the expression profile.

Conclusion: These data indicate that the MAPK pathway may be pivotal to the transition from AK to cSCC, thus representing a potential target for cSCC prevention. In addition, transcriptome differences identified between cSCC subtypes have important implications for future development of targeted therapies for this malignancy.

Figure 1

Heat map of 239 overlapping differentially expressed probes identified by ANOVA and eBayes analysis of cSCC vs AK. Characterisation bars beneath the dendrogram highlight key clinicopathological variables. Abbreviations: AK= actinic keratosis; IC= immunocompetent; IS= immunosuppressed; MD= moderately differentiated; PD= poorly differentiated; SCC= squamous cell carcinoma; WD= well differentiated.

Figure 2

qRT-PCR analysis of 12 differentially expressed genes between AK and cSCC. Solid black squares indicate outlier samples. For the purposes of comparison, the cSCC has been split into WD and MD categories, as well as overall values (SCC). Abbreviations: AK= actinic keratosis; MD= moderately differentiated; SCC= squamous cell carcinoma; WD= well differentiated.

Figure 3

Enrichment of differences in the MAPK signalling pathway (HSA04010) between AK and cSCC as identified by GSEA, and cluster analysis of cSCC. (A) Enrichment of genes in the MAPK signalling pathway. The blue line indicates the enrichment score (ES) and the black vertical lines beneath correspond to individual genes within the set, ranked according to their enrichment. If no enrichment was present, then the genes would be distributed equally from left to right. (B) Heat map of the enriched genes, showing their level of expression across AK and cSCC. Red indicates high expression and green indicates low expression. Each row corresponds to a gene within the MAPK gene set, while each column corresponds to an individual sample. (C) Cluster dendrogram revealing two main clusters of cSCC, separated predominantly by differentiation status (WD vs M/PD). Abbreviations: AK= actinic keratosis; IC= immunocompetent; IS= immunosuppressed; MD= moderately differentiated; PD= poorly differentiated; SCC= squamous cell carcinoma; WD= well differentiated.