Spatial Transcriptomics Shows a Distinctive Tumour Microenvironment in the Invasive Versus Premalignant Portion of Early Cutaneous Squamous Cell Carcinoma

Cutaneous squamous cell carcinoma (SCC) is known for its stepwise progression from healthy skin to premalignant actinic keratosis (AK), followed by a malignant transformation to SCC. Unfortunately, less attention has been paid to changes in gene expression in the tumour microenvironment during this process. We retrospectively selected early-stage cutaneous SCC tissue samples containing both invasive and premalignant portions and conducted a spatial transcriptomic experiment using a NanoString GeoMx Digital Spatial Profiler (DSP). First, we selected invasive and premalignant regions of interest (ROIs) for each tissue. We then compared the gene expression patterns between the two portions (invasive versus premalignant) of the three segments: tumour cells, immune cells and fibroblasts, in each ROI. As a result, early-stage cutaneous SCC tissue samples from 17 patients were selected for this study. We identified 29, 14 and 15 differentially expressed genes (DEGs) between the invasive and premalignant portions of the tumour cells, immune cells and fibroblasts, respectively. The top three genes with the highest absolute log₂ fold-change were CCDC88C, GJD3 and COMP in tumour cells; SVEP1, TSLP and PPP2R5C in immune cells; and SPAG6, PPP1CA and CCDC68 in fibroblasts. Notably, several genes, such as COMP, SVEP1 and SPAG6, have been linked to the development and function of cancer-associated fibroblasts. Functional enrichment analysis revealed that several pathways were altered in tumour and immune cells. In conclusion, distinctive changes in gene expression patterns were observed as AK progressed to SCC.