Abstract Introduction and aims Cutaneous squamous cell carcinoma (cSCC) is one of the most common cancers, with well-established risk factors including immunosuppression and ultraviolet (UV)B exposure. Although only 2–4% of patients develop metastatic disease, metastasis sharply worsens survival and drives treatment complexity. Understanding the molecular changes that enable metastatic spread is therefore essential. This study aimed to characterize the transcriptomic evolution of cSCC metastasis from their corresponding primary tumours. Methods In total, 488 formalin-fixed paraffin-embedded samples were collected from a retrospective cohort of immunocompetent patients with cSCC, including primary tumours, metastatic lesions (∼ 90% lymph node, 10% skin) and normal perilesional skin ≥ 2 mm from tumour. Primary tumours were classified as nonmetastasizing if patients had ≥ 3 years of follow-up without metastasis. Dermatopathologist-annotated samples underwent TempO-Seq profiling. Differential expression analyses were performed using DESeq2 across key stages of disease progression, including nonmetastasizing vs. metastasizing primaries, and primary tumours vs. matched or unmatched metastases. Cell-type deconvolution was performed using CIBERSORT with publicly available single-cell reference datasets and samples were ranked using a published ‘differentiated vs. progenitor’ transcriptional signature. Results Metastasizing primary tumours demonstrated 326 upregulated and 628 downregulated genes compared with nonmetastasizing primaries. Metastases had 243 upregulated and 396 downregulated genes compared with matched primaries; however, when controlling for tissue type, this narrowed to only two upregulated and 22 downregulated genes. Samples became progressively more progenitor-like along the disease continuum. Cell-type deconvolution identified dynamic shifts in cellular composition accompanying progression. Conclusions Primary tumours that metastasize are transcriptionally distinct from primary tumours that do not metastasize yet are remarkably transcriptionally similar to their matched metastases. This suggests that the metastatic phenotype may be largely pre-established within the primary lesion. Rather than acquiring new capabilities, some cSCCs may have metastatic potential encoded during primary tumour development.
Hurley et al. (Tue,) studied this question.