Combination of Quizartinib and Omacetaxine Mepesuccinate (QUIZOM) As an Effective Treatment Remodels Proteostasis and Triggers Inflammatory Response in FLT3-ITD AML

Background FMS-like tyrosine kinase-3 internal tandem duplication (FLT3-ITD) is one of the most common mutations in AML and is associated with inferior prognosis. FLT3 inhibitors have been approved for treatment of AML but relapse is frequent. In silico analysis of public datasets has identified protein translation as a vulnerable target in this AML subtype. We also previously reported in vitro and in vivo efficacy of combining FLT3 inhibitor and protein translation inhibitor in treatment of FLT3-ITD AML. In this study, we examined the combination effects of QUIzartinib and OMacetaxine mepesuccinate (OM), a protein translation inhibitor in FLT3-ITD AML based on laboratory studies, clinical trial and single cell transcriptomic analysis. Methods Adult patients with relapsed or refractory (R/R) FLT3-ITD AML or those unfit for conventional chemotherapy were recruited in a Phase II single-arm open-label clinical trial and treated with quizartinib 30 mg daily and OM 2 mg daily at 7 days (5-day subsequently) per 28-day cycle until haematopoietic stem cell transplantation (HSCT) or disease progression. Therapeutic mechanism of QUIZOM was evaluated by transcriptome and translatome analyses of FLT3-ITD cell lines and primary AML samples. Single-cell RNA sequencing of serial BM samples from patients receiving QUIZOM was examined. Results In 40 FLT3-ITD AML, composite complete remission (CRc) rate was 83%. Thirteen patients were bridged to allogeneic HSCT. All patients without HSCT relapsed. Median LFS and OS were 10 and 12.9 months respectively. At a median follow up of 4.7 years, median LFS and OS were not reached for post-HSCT patients. Treatment was generally tolerated with Grade 3/4 cytopenia (68%) and febrile neutropenia (60%) as the common adverse events. Transcriptome analysis and translatome profiling of newly synthesised proteins in QUIZOM-treated FLT3-ITD AML cell lines showed disruption in mitochondrial metabolism and chaperone-mediated protein folding pathways. These led to formation of protein aggregates, induction of apoptosis, DNA damage response, senescence associated secretary phenotype (SASP) and cGAS-STING pathway activation. Single-cell RNAseq of clinical samples demonstrated a more drastic decrease in HSC-MPP population and expansion of immune populations (CD4 & CD8 T, NK/T and NK cells) in responders, in addition to elevated T-bet activity and increased number of differentiated effector memory T cells. In clinically resistant samples, HSC-MPP cells carrying FLT3-ITD mutations leukemic stem cell (LSC) markers (CD34+CD44+CD69+) persisted and showed activated JNK pathway and lipid metabolism. Therapeutic targeting of JNK and lipid metabolism by C-Fos/C-Jun and CPT1a inhibitors restored QUIZOM sensitivity in primary FLT3-ITD samples in vitro. Conclusions QUIZOM is a novel treatment option for FLT3-ITD AML that effectively eliminates FLT3-ITD leukemic cells and activates immune populations. Clinical resistance is associated with persistence of the LSC population and might be overcome by targeting JNK pathway and lipid metabolism.