MPN-inducing mutations as biomarkers of synthetic lethality

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Myeloproliferative neoplasms (MPNs) such as polycythemia vera (PV), essential thrombocythemia (ET), and primary myelofibrosis (PMF) often carry JAK2(V617F), MPL(W515L) and mutations in calreticulin (CALRmut). These aberrations may be accompanied by mutations in TET2, ASXL1, DNMT3A, EZH2, and other genes further complicating utilization of MPNs genetic/epigenetic signatures as potential biomarkers for therapeutic decisions. Current treatment options for MPNs include myelosuppressive therapy in the form of hydroxyurea and JAK1/2 inhibitor QAK1/2i) ruxolitinib. MPNs can have prolonged chronic phases, but may eventually accelerate and transform into a secondary acute myeloid leukemia that is ultimately fatal. Therefore, it is imperative to generate new therapies that alone or in combination with already approved drugs could potentially extend the complete remission time and/or be used in patients which progressed to the malignant stage. Since all 3 "main" mutations [JAK2 (V617F), CALR(del52), and MPL(W515L)] were found in MPN stem cells (MPNSCs) these cells must be eliminated in order to improve therapeutic outcome. Unfortunately, the potential therapeutic approaches against MPNSCs are limited. MPN cells, including MPNSCs accumulate potentially lethal DNA double-strand breaks (DSBs), which are repaired by two major mechanisms, BRCA-mediated homologous recombination (HR) and DNA-PK -mediated non-homologous end-joining (D-NHEJ). HR and D-NHEJ repair DSBs in proliferating cells and D-NHEJ plays a major role in quiescent cells. PARP1 -dependent back-up NHEJ (B-NHEJ) serves as back-up in both proliferating and quiescent cells. Cancer-specific defects in DSB repair create the opportunity to employ synthetic lethality, e.g. elimination of BRCA1/2-mutated cancer cells by PARP1 inhibitor (PARP1i). However, BRCA1/2 mutations are rare in MPNs. We hypothesize that MPN-inducing mutations are prognostic biomarkers of therapeutic synthetic lethality triggered by DNA repair inhibitors. We will determine if specific MPN-inducing mutation(s) (biomarkers) predispose quiescent and/or proliferating MPN stem and progenitor cells from individual patients to PARP1i-induced synthetic lethality combined with the inhibitors of HR and D-NHEJ (Aim #1) or with JAK2i (Aim #2). We will also employ murine knockin/knockout models of MPNs and primary MPN xenografts in humanized immunodeficient mice to determine if DNA repair inhibitors and/or JAK2i exert anti-MPN synthetic lethal effect in pre-clinical settings (Aim #3).