Project Abstract Malignant peripheral nerve sheath tumors (MPNSTs) represent a group of highly aggressive soft tissue sarcomas that occur in distinct clinical settings: neurofibromatosis 1 (NF1)-associated (45%), sporadic (45%) or radiotherapy (RT)-associated (10%). MPNSTs metastasize early and are resistant to radiotherapy and systemic chemotherapy and have poor prognosis. Irrespective of the clinical settings, MPNSTs share the same molecular pathway inactivation in NF1 (>90%, hence NF1-deficient), Polycomb repressive complex 2 (PRC2), and CDKN2A through biallelic genetic alterations, suggesting that they can be molecularly targeted similarly. NF1- deficient plexiform neurofibroma responds well to MEK inhibitor (MEKi) treatment clinically; however, NF1- deficeint MPNSTs arising from plexiform neurofibromas are universally resistant to MEKi, suggesting intrinsic resistance in the more aggressive form of peripheral nerve sheath tumors. Using MPNST patient tumor samples and preclinical MPNST models, we have uncovered that PRC2-loss leads to PDGRA upregulation; MEKi treatment resulted in feedback upregulation of PDGFRB irrespective of the PRC2 status. The convergence of the PDGFR pathway activation by different mechanisms points to a novel therapeutic opportunity to target the PDGFR pathway to overcome MEKi resistance in MPNST. Combination of a novel PDGFRA/B inhibitor, ripretinib with a MEKi leads to synergistic growth inhibition of MPNST in vitro and in vivo. We hypothesize that PDGFRA/B pathway activation represent a central resistance mechanism to MEKi and combined targeting of the PDGFR and MAPK pathways with ripretinib (pan-PDGFRA/B inhibitor) and binimetinib (MEKi) may present an effective therapeutic strategy in NF1-deficient MPNST. Here, we propose to investigate the tumor heterogeneity and cellular plasticity involved in tumor evolution and adaptive resistance to binimetinib and combination of ripretinib and binimetinib, using well-defined preclinical MPNST in vitro and in vivo model systems and single-cell analysis including single cell RNA-seq (scRNA-seq) and a novel barcoding system. Additionally, we propose a collaborative clinical investigation between CCR/NCI (Drs. Widemann/Shern) and MSKCC (Dr. Chi) to conduct a proof-of-concept phase I/II study of the combination of ripretinib and binimetinib in patients with NF1-deficient MPNST. In this trial, we will assess and optimize the evaluation of MAPK pathway inhibition to the ripretinib/binimetinib combination therapy using traditional ERK phosphorylation and newly established custom Pea3-family ETS-regulated MAPK signature. Further, we will also investigate the tumor heterogeneity and cellular plasticity in tumor evolution and resistance mechanisms to the ripretinib/binimetinib combination using targeted NGS, scRNA-seq and integrative analysis. The proposal leverages the synergistic expertise and resources at MSKCC and CCR/NCI. We believe that these studies will generate mechanistic insight of therapeutic resistance and provide the pivotal clinical and translational information for future definitive trials, with the potential to change the clinical practice in MPNST.

Project Narrative Malignant peripheral nerve sheath tumors (MPNSTs) represent a group of highly aggressive soft tissue sarcomas with poor prognosis that occur in distinct clinical settings: neurofibromatosis 1 (NF1)-associated (45%), sporadic (45%) or radiotherapy (RT)-associated (10%). Most MPNSTs have NF1 loss (>90%hence, NF1- deficient), CDKN2A loss (~80%) and PRC2 loss (~60-80%), but they are resistant to MEK inhibitor alone due to feedback reactivation of PDGFRA/B pathways. Here, we propose a phase I/II study of a novel combination of ripretinib and binimetinib that targets both the PDGFR and MAPK pathways in patients with NF1-deficeint MPNSTs and to evaluate for biomarkers for MAPK pathway inhibition, as well as to investigate the MPNST tumor heterogeneity and plasticity during tumor evolution and in response to combination treatment using single cell analysis.