Pharmacologic degradation of WDR5 suppresses oncogenic activities of SS18-SSX and provides a therapeutic of synovial sarcoma [CUT&Tag]

Disease-causing aberrations of childhood cancers recurrently target the chromatin pathway genes leading to epigenetic dysregulation. For example, almost 100% of patients with synovial sarcoma (SS) carry an abnormal gene fusion termed SS18-SSX, which produces a disease-specific oncofusion protein that is incorporated into the SWI/SNF chromatin-remodeling complex and profoundly alters its functionalities. Thus, targeting epigenetic dependencies in childhood cancer holds great promise for improving current treatment of the affected patients. Leveraging on the cancer cell dependency dataset, medicinal chemistry tool compounds and genomic profiling approaches, we here show WDR5, a chromatin factor involved in the deposition of histone H3 lysine 4 (H3K4) methylation, to be an unexplored vulnerability of SS. Mechanistically, WDR5 and SS18-SSX associate with one another and colocalize significantly at the target oncogenes where WDR5 is essential for optimal chromatin binding of the SS18-SSX-containing chromatin modelers. Using the WDR5-targeted Proteolysis Targeting Chimera (PROTAC) compound, we further show that pharmacologic degradation of WDR5 in SS cells not only suppressed the SS18-SSX-related oncogenic gene-expression programs but additionally led to p53 activation and tumor cell senescence through downregulation of ribosomal proteins (RPs) and activation of nucleolar stress response. Importantly, the WDR5-targeted PROTAC significantly suppressed malignant growth of SS in vitro and in vivo. Taken together, we report WDR5 as a SS dependency and demonstrate the WDR5 PROTAC degrader to be a promising strategy for the treatment of SS. We used CUT&Tag to assess the genome-wide binding of WDR5, SS18-SSX, BAF155, H3K4me2, H3K4me3 and/or H2AK119ub1 in cells (HSSY II, SYO1 and/or U2OS), either parental, or mock- or compound-treated, or stably transduced with a previously reported shRNA targeting SSX (shSSX) or a scramble control (shScr).