Transcriptomic profiling of tumor infiltrating cells in cutaneous squamous cell carcinoma using single-cell rna sequencing

Cutaneous Squamous Cell Carcinoma (cSCC) is the second most common skin cancer, arising from keratinocytes of the epidermis. Tumor infiltrating lymphocytes and monocytes (TILs and TIMs) have been implicated in driving tumor growth, invasion, metastasis, and response to therapy. However, little is known about the role of TILs and TIMs in cSCC. We applied single-cell RNA sequencing (scRNA-seq) to better understand cSCC tumor infiltrating cell heterogeneity. Single cell suspensions were prepared from healthy epidermis, perilesional epidermis, and metastasized cSCC tumor (total 6 samples). Using 10xGenomic Chromium 3’ reagent kits, we generated scRNA-Seq libraries from sorted CD45+ immune cells. We then profiled the transcriptomes of ∼22,000 cells, which were then analyzed by canonical correlation analysis and the CIBERSORT decomplexation platform. As expected, tissue resident immune cells in healthy epidermis are primarily Langerhans cells (LC) with a very small subset of T cells. The frequency of LCs in perilesional epidermis was dramatically reduced, as TILs and TIMs had infiltrated the area. Infiltrating cells in cSCC tumor body are more diverse, including a large proportion NK cells, four T cell subtypes, several macrophage/monocyte subsets, mast cells, and B cells. Notably, the tumor samples lack LC. The proportions of these cells vary between patients, but the clinical relevance of this is unclear. The cells identified here may represent new clinical targets for the treatment of metastatic or locally advanced cSCC patients for which resection or radiation are not possible