A single-cell atlas of human soft tissue sarcoma ecosystems with focus on mechanisms of immune evasion

Soft tissue sarcomas (STS) are rare, aggressive cancers. About 50% of patients with high-risk STS die within 5 years after diagnosis, highlighting the need for novel treatment approaches. A major obstacle for novel treatment design is our limited understanding of STS as ecosystems, shaped by diverse tumor cells and their interactions with cells of the microenvironment. Emerging strategies that target cellular relationships in STS are promising, such as immune checkpoint inhibition. First clinical trials assessing immune checkpoint inhibition were promising, but success varied greatly among different STS subtypes and a rational selection of patients was not available. A comprehensive description of the complex cellular diversity and interactions in STS tumor ecosystems and links to disease progression are currently missing. Here we will combine simultaneous detection of single-cell transcriptomes and cell surface proteins with 32-plex immunofluorescence imaging to characterize STS tumor and immune cell diversity with single-cell spatial resolution in seven STS subtypes. The STS subtypes include dedifferentiated liposarcoma, Ewing sarcoma, myxoid/round cell liposarcoma, clear cell sarcoma, desmoplastic small round cell tumor, fibromyxoid sarcoma, and solitary fibrous tumor, present with poor prognosis and are promising candidates for immunotherapies. Objectives are (1) to characterize the cellular diversity and tumor-immune interactions in STS ecosystems using simultaneous single-cell transcriptomics and cell surface proteomics, (2) to profile the STS immunoenvironment with single-cell spatial resolution in situ, and (3) to functionally assess candidate tumor-immune interactions in vitro. This project will provide the first single-cell atlas for seven STS subtypes and will enable a better understanding of STS tumor ecosystems, pave the way for novel precision oncology approaches, and facilitate the identification of candidates for immunotherapy clinical trials.