Project 3: Identifying Targetable Epigenetic and Immuno-Oncologic Vulnerabilities in Synovial Sarcoma

RP3: Identifying Targetable Epigenetic and Immuno-Oncologic Vulnerabilities in Synovial Sarcoma ABSTRACT Synovial sarcoma (SS) is driven by SS18::SSX-dependent chromatin dysregulation, suggesting that elucidating key aspects of this deregulation might point to therapeutic epigenetic vulnerabilities. At the same time, driver fusions such as SS18::SSX may generate a unique class of shared, or public, neoantigens because they create novel peptide sequences that diverge significantly from self-proteins. Specifically, the junctional amino acid sequence of the chimeric SS18::SSX proteins is unique to SS cells. In addition, there is evidence that epigenetic modulation may potentiate immunotherapy approaches. Thus, our overall goal is to identify epigenetic and immuno-oncologic vulnerabilities in SS and potential synergies between them towards an overall goal of long- term responses in metastatic SS. To accomplish this, our multidisciplinary research team of experts in cancer genomics and epigenetics, T cell immunobiology and immune-peptidomics, and clinical trials in pediatric and young adult sarcomas will pursue 3 specific aims. Aim 1 is to decipher H3K36 methylation-dependent crosstalk and vulnerabilities in SS, on the basis of our clinical genomic profiling data on SS identifying recurrent loss of function in histone 3 lysine 36 (H3K36) methyltransferases (e.g. SETD2) in ~10% of cases. In isogenic cell lines, we will determine how decreased H3K36me3 affects the genomic localization of SS18::SSX and fusion protein- dependent transcriptional programs and establish the key determinants of DNA methylation and polycomb- mediated chromatin domains. We will validate these observations in prospectively collected patient-derived tissues and xenografts (PDXs). Finally, we will identify SETD2-/--specific dependencies in SS using a chemical probe approach; resulting hits will be studied mechanistically and validated in both PDXs and isogenic SETD2-/- models. Because epigenetic mechanisms are important tumor-intrinsic mediators of immune escape, we will also explore whether SETD2 loss affects SS immunogenicity. Aim 2 is to measure the immunogenicity of an SS18::SSX public neoantigen and test the antitumor efficacy of T cells genetically engineered with a T cell receptor recognizing it. Specifically, we will define the HLA-restricted immunogenic peptides resulting from the SS18::SSX fusion protein, retrieve the TCR α/β gene sequences associated with SS patient-derived T cells that recognize such peptides, and validate that cloned TCRs confer fusion-derived reactivity and tumor regression in vivo when retrovirally transduced into a polyclonal T cell population. In Aim 3, we will determine the tolerability, immunogenicity, and antitumor efficacy of a multivalent mRNA vaccine encoding the SS18::SSX(1/2) junction sequence and multiple cancer-testis antigens (CTAs) highly expressed in SS, in combination with an anti-PD-L1 antibody, via a phase I/II clinical trial in collaboration with Moderna and TRACON. Correlative analyses associated with the trial will measure how the vaccine affects the T cell response to polypeptides containing the above sequences and resolve the HLA restriction and TCR clonotypes for T cells responding to the SS18::SSX fusion and CTA sequences.