Combinatorial Genetics Uncovers Novel Targets for the Treatment of Npm1/Cohesin Mutated AML
Authors: Meyer Alison E , Stelloh Cary , Fisher Joseph B , Pulakanti Kirthi , Vassiliou George S. , Viny Aaron D , Levine Ross L. , Rao Sridhar 
Published: October 2019

Abstract
Current precision medicine approaches typically target a single genetic mutation. However, adult acute myeloid leukemia (AML) is difficult to treat due to its genetic complexity. Approximately 30 somatic mutations have been found to be recurrent, with an average of 5-15 mutations present per patient (Cancer Genome Atlas 2013). Therefore, combinatorial genetic approaches have the power to uncover novel gene targets that can be used to tailor therapies to an individual's unique mutational spectrum. Mutations in NPM1 commonly occur in in AML. Approximately 25-30% of patients harbor a specific variant of the NPM1 mutation referred to as NPM1cA, which results in mislocalization of the Npm1 protein from the nucleus to the cytoplasm (Cancer Genome Atlas 2013; Falini 2005). While NPM1cA is considered to be a driver of AML development, mice with this mutation develop AML with a long latency (18 months) and with incomplete penetrance (Vassiliou 2011). In addition, those mice that do develop AML acquire additional genetic mutations, suggesting that NPM1cA cooperates with serially acquired mutations to drive AML development (Dovey 2017).
It was recently discovered that mutations in the cohesin complex (consisting of the genes STAG2, SMC1A, SMC3, and RAD21) are also common in AML, with mutation in any of the four components resulting in haploinsufficiency (Cancer Genome Atlas 2013). Cohesin haploinsufficiency is enriched in patients with NPM1 mutations. Although cohesin mutations alone are insufficient to generate AML in mice (Viny 2015), they do result in increased hematopoietic stem and progenitor cell (HSPC) self-renewal (Mazumdar 2015; Fisher 2017). As the cohesin complex has known roles in chromosomal organization and the regulation of gene expression, we hypothesized that cohesin mutations would cooperate with NPM1cA to uniquely alter gene expression, resulting in AML. We crossed inducible NPM1cAflox/+ and SMC3flox/+ mouse models to examine this genetic interaction.
Our current data show that the double mutant mice develop AML with increased penetrance compared with the Npm1cA/+ mice alone, with a trend toward decreased latency. The double mutant HSPCs also exhibit increased self-renewal in vitro compared to the Npm1cA/+ or SmcΔ/+ single mutants. To examine changes in gene expression, we performed RNA sequencing on lineage-depleted bone marrow in 3 mice from each genotype (WT, Npm1cA/+, Smc3Δ/+, and double) 4 weeks post excision. Consistent with our hypothesis, additive changes in gene expression were not observed. Instead, a unique set of genes were found to be deregulated in Npm1cA/+; Smc3Δ/+ marrow.
In an effort to specifically target Npm1cA/+; Smc3Δ/+ mutant AML, we screened our list of uniquely-affected genes for those associated with AML. We found DOCK1 to be overexpressed in the double, but not Npm1cA/+ single, cells. High expression of this gene has been correlated with decreased overall and disease-free survival in AML patients (Lee 2017). To determine if DOCK1 contributes to the enhanced cell growth observed in vitro in our leukemic lines, we used an inhibitor that targets Dock1. This inhibitor induced apoptosis in our double leukemic cell lines but was less effective in our NPM1 single mutant or WT cells. Additionally, no effect was observed with a genetically unrelated AML line, MLL-AF9. Similarly, shRNA-mediated knockdown of Dock1 resulted in decreased cell viability in Npm1cA/+; Smc3Δ/+ leukemic lines but not in Npm1cA/+ only lines. We thus hypothesize that Dock1 represents a unique target for the treatment of patients harboring the Npm1/Cohesin mutational combination. Our results provide validity to the concept that combinatorial genetics can be used to target the unique genetic landscape of an individual patient. Future studies will focus on the impact of Dock1 inhibition in human Npm1/Cohesion mutated AML cell lines.

Disclosures
Vassiliou: KYMAB: Consultancy, Equity Ownership; Celgene: Research Funding. Levine:Isoplexis: Equity Ownership; Epizyme: Patents & Royalties; Imago: Equity Ownership; Loxo: Consultancy, Equity Ownership; Janssen: Consultancy, Honoraria; Gilead: Honoraria; Prelude: Research Funding; Novartis: Consultancy; Celgene: Consultancy, Research Funding; Roche: Consultancy, Research Funding; C4 Therapeutics: Equity Ownership; Qiagen: Equity Ownership, Membership on an entity's Board of Directors or advisory committees.