Signatures of EMT, immunosuppression and inflammation of primary and recurrent human cutaneous squamous cell carcinoma at single-cell resolution

AbstractThe recurrence of cutaneous squamous cell carcinoma (cSCC) after surgery remains a key factor affecting cSCC outcomes, which is related to the reprogramming of the tumour microenvironment (TME). Herein, we utilized single-cell RNA sequencing (scRNA-seq) to examine the dynamic changes in epithelial cells, T cells, myeloid cells and fibroblasts between primary and recurrent cSCC. We uncovered the immunosuppressed microenvironment in recurrent cSCC, which exhibited a T-cell- excluded and SPP1+ TAM-enriched status. In recurrent cSCC, CD8+ T cells showed high exhaustion and low inflammatory features, while SPP1+ TAMs displayed global protumour characteristics, including decreased phagocytosis and inflammation as well as increased angiogenesis. Furthermore, we found that the subgroups of SPP1+ tumour- associated macrophages (TAMs) harboured distinct functions. SPP1+ CD209high TAMs showed obvious features of phagocytosis, while SPP1+ CD209low TAMs tended to have a high angiogenic ability. A subpopulation of tumour-specific keratinocytes (TSKs) showed significant epithelial–mesenchymal transition (EMT) features in recurrent cSCC, which might be due to their active communication with IL7R+ cancer-associated fibroblasts (CAFs). In addition, we found that MDK could provoke different cell–cell interactions in cSCCs with distinctive staging. In primary cSCC, MDK was highly expressed in fibroblasts and could promote their proliferation and block the migration of tumour cells, while in recurrent cSCC, the high expression of MDK in TSKs promotes their proliferation and metastasis. Overall, our study provides insights into the critical mechanisms of cSCC progression, which might facilitate the development of a powerful system for the prevention and treatment of cSCC recurrence.