Opposing genetic and immune mechanisms shape oncogenic programs in synovial sarcoma

Synovial sarcoma (SyS) is an aggressive neoplasm driven by the SS18-SSX fusion, and characterized by low T cell infiltration. Here, we studied the cancer-immune interplay in SyS using an integrative approach that combines single-cell RNA-seq (scRNA-seq), spatial profiling, genetic and pharmacological perturbations. scRNA-Seq of 16,872 cells from 12 human SyS tumors uncovered a malignant subpopulation that marks immune deprived niches in situ and marks tumors with poor clinical outcomes in three independent cohorts. Functional analyses revealed that this malignant cell state is controlled by the SS18-SSX fusion, repressed by cytokines secreted by macrophages and T cells, and can be synergistically targeted with a combination of HDAC and CDK4/6 inhibitors. This drug combination enhanced malignant cell immunogenicity in SyS models, leading to induced T cell reactivity and T-cell-mediated killing. Our study provides a blueprint for investigating heterogeneity in fusion-driven malignancies and demonstrates an interplay between immune evasion and oncogenic processes that can be co-targeted in SyS and potentially in other malignancies. Individual cells were dissociated from fresh tumor resections and profiled with a modified full length SMART-Seq2 protocol and with a droplet-based (10x) approach. Raw data is to be made available through DUOS (controlled access) due to patient privacy concerns.