Formalin-fixed, paraffin-embedded (FFPE) skin specimens were obtained from a cohort of three patients with cutaneous squamous cell carcinoma (cSCC). For each patient, tissue blocks contained histologically distinct regions corresponding to (i) healthy skin, (ii) peritumoral skin, (iii) actinic keratosis (AK) and/or in situ cSCC, (iv) advanced tumor core, (v) advanced invasive cSCC. Hematoxylin and eosin–stained sections were reviewed by a board-certified dermatopathologist to confirm diagnoses and to guide region selection. Spatial transcriptomics was carried out through the Nanostring Technologies GeoMx Digital Spatial Profiling (GeoMx DSP). The protocol has five steps: standard FFPE tissue preparation; tissue incubation with a mixture of visualization markers (VMs) and DSP probes; imaging and region of interest (ROI) selection; ultraviolet (UV) exposure; and oligo collection step. This is then quantified using the Nanostring nCounter® system. Briefly, tissue sections were stained with a CD68/PanCK/Vimentin/Sytox panel to visualize tissue architecture and guide the selection of regions of interest (ROIs) for analysis. For each slide, ROIs were drawn in order to analyze the expression of the WTA gene panel in the healthy regions, AK/cSCC in situ, advanced cSCC, and invasive front. Each ROI was further segmented in 3 to 5 AOIs (area of illumination) based on the PanCK, CD68, and Vimentin staining. AOIs enriched for PanCK marked epithelial/tumor regions; CD68-enriched AOIs captured macrophage-rich regions; and PanCK⁺/Vimentin⁺ AOIs were used as an operational proxy for the invasive front, consistent with the local histopathology. The gene expression of each AOI was analyzed on the GeoMX DSP (NanoString®) using the Whole Transcriptome Atlas (WTA) panel. This panel covers the expression of 18695 protein-coding genes. Slides were incubated overnight with in situ hybridization (ISH) probes conjugated to unique DNA indexing-oligonucleotides via a UV-photocleavable linker. Each AOI was then illuminated with a UV laser to precisely release and collect the DNA barcode in a 96-well plate. GeoMx DSP aspirates in the plate contain photocleaved DNA oligos comprised of an analyte identifier, a unique molecular identifier (UMI) barcode, and primer binding sites. A PCR was performed on these aspirates to add Illumina adapter sequences and unique dual sample indices.