The chromatin landscape of primary synovial sarcoma organoids is linked to specific epigenetic mechanisms and dependencies [ChIP-seq]

Synovial sarcoma (SyS) is an aggressive mesenchymal malignancy invariably associated with the chromosomal translocation t(X:18; p11:q11), which results in the in-frame fusion of the BAF complex gene SS18 to one of three SSX genes. Fusion of SS18 to SSX generates an aberrant transcriptional regulator, which, in permissive cells, drives tumor development by initiating major chromatin remodeling events that disrupt the balance between BAF-mediated gene activation and Polycomb-dependent repression. Here, we developed SyS organoids and performed genome-wide epigenomic profiling of these models and mesenchymal precursors to define SyS-specific chromatin remodeling mechanisms and dependencies. We show that SS18-SSX induces broad BAF domains at its binding sites, which oppose Polycomb Repressor Complex (PRC) 2 activity while facilitating recruitment of a non-canonical (nc)PRC1 variant. Along with the uncoupling of Polycomb complexes, we observed H3K27me3 eviction, H2AK119ub deposition and the establishment of de novo active regulatory elements that drive SyS identity. These alterations are completely reversible upon SS18-SSX depletion and confer vulnerability to USP7 loss, a core member of ncPRC1.1. SyS organoids thus provide a powerful model to define mechanisms of epigenetic dysregulation on which SyS cells are dependent. ChIP-seq for the BAF complex subunit SMARCA2 and histone marks in synovial sarcoma and Ewing sarcoma spheroids, human pediatric mesenchymal stem cells (MSCs), MRC5 and MET5A cells. ChIP-seq for the BAF complex subunit SMARCA2 and histone marks in mouse C3H10T1/2 cells. V5-tagged SYT-SSX was expressed in C3H10T1/2 cells using a lentiviral expression vector and ChIP-seq was performed using an anti-V5 antibody. C3H10T1/2 cells expressing V5-SYT-SSX were further lentivirally induced with a control vector (pLKO) or a CRE recombinase (CRE) to knock-out the sequence encoding SYT-SSX. Please note that the raw data from primary patient cells (GSM4477549-GSM4477588, GSM4477595-GSM4477600) cannot be released in GEO due to patient privacy concerns and will be submitted to dbGaP.