Single-Cell Sequencing Reveals Novel Tumor Populations and Their Interplay with the Immune Microenvironment in a Pleomorphic Rhabdomyosarcoma

Pleomorphic rhabdomyosarcoma is a rare soft-tissue tumor that occupies an uncertain middle ground between rhabdomyosarcoma and undifferentiated pleomorphic sarcoma. With its relative rarity, aggressiveness, and lack of detailed characterization, it presents a challenging task for therapeutic treatment. In this case study, we use single-cell transcriptomics to investigate the heterogeneous landscape of pRMS and the tumor microenvironment. We demonstrate that the tumor populations in pRMS have a clear division into myogenic and non-myogenic clusters, with the non-myogenic clusters having more numerous communication links with the immune populations. All pRMS tumor clusters use the MIF-CD74 pathway to suppress the immune response, while APP, PTN, and CXCL12 signaling are employed predominantly by the non-myogenic tumor clusters. The cytotoxic T cells in pRMS bear markers of exhaustion (LAG3, HAVCR2, EOMES), and the macrophages express myeloid checkpoint-related genes (SIGLEC1, SIRPA, CSF1R, HAVCR2). This transcriptomic data suggests that targeting MIF and APP signaling in pRMS may have therapeutic potential; however, studies on multiple-patient cohorts, protein verification, and in vitro and in vivo validation are still needed for clinical actionability.