Biology and Prognostic Implications of FLT3 Mutations in AML

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DESCRIPTION (provided by applicant): AML is a highly aggressive type of leukemia that is defined by its genomic complexity. Mutations of the FLT3 gene (FLT3/ITD or FLT3/ALM) are the most common somatic mutations in AML, and those with FLT3/ITD have a high risk of failure and poor outcome. We have established the clinical implications of FLT3 mutations in AML and have implemented risk-based therapy allocation using FLT3 mutation status. Despite initial utility of FLT3 inhibitors as directed therapy targeting FLT3 mutations, rapid evolution of drug resistance and resultant lack of survival benefit of FLT3 inhibitors requires evaluation of cause of failure and mechanism of drug resistance in patients with FLT3 mutations. Defining the mechanism of drug resistance and devising strategies to circumvent or treat the resistant phenotype would help convert this most aggressive type of AML into a curable one. Our studies into the biology and prognostic significance of FLT3 mutations have implicated several mediators of resistance, including evolution of acquired uniparental disomy (aUPD), newly acquired secondary mutations, as well as structural variation of the ITD (ITD length and novel FLT3 transcript variants) that need to be evaluated and confirmed. The overarching goal of this grant is to build on the data generated in the last 5 years to further our understanding of FLT3 biology, and mechanism of disease resistance in order to devise means of better targeting this gene for therapeutic purposes. We have created specific experimental tools and collected patient resources to aid in this endeavor, including generation of two sorafenib resistant cell lines, cloning of FLT3/ITDs of different ITD fragment lengths and creation of repository of primary patients specimens refractory to FLT3 inhibitors or to conventional chemotherapy. In this proposal, we aim to initially investigate the newly discovered disease-associated FLT3 transcript variants in AML. These novel variants (cryptic and skipped exons) have significant potential to alter the function of the gene and impact its biologic and clinical significance and is response to FLT3 inhibitors. In addition, we will utilize our laboratory generated resistant cell lines as well as our relapsed/refractor patient specimens and thru whole genome sequencing, screen for novel genomic alterations that may have led to the emergence of drug resistance. Using high throughput shRNA screening will identify genes and pathways that can be used to circumvent drug resistance or re-sensitize the resistant cells. Finally, we have demonstrated that in patients with FLT3/ITD, aUPD and ITD length are highly associated with relapse. We will use AAV-mediated gene targeting to knock in ITDs of different lengths in a heterozygous fashion and determine whether presence of FLT3/ITD is sufficient for evolution of aUPD. In addition, using designed lentiviral vectors, we will assess the role of ITD length in conferring drug resistance. The data from this proposal will provide significant insight into the mechanism of drug resistance in FLT3 mutant AML and is likely to lead to new tools for incorporation into clinical trials and identification of biologic pathways that can be targeted for therapeutic purposes.