Dasatinib response in acute myeloid leukemia is correlated with FLT3/ITD, PTPN11 mutations and a unique gene expression signature

Abstract

Novel targeted therapies demonstrate improved survival in specific subgroups (defined by genetic variants) of acute myeloid leukemia (AML) patients, validating the paradigm of molecularly targeted therapy. However, identifying correlations between AML molecular attributes and effective therapies is challenging. Recent advances in high-throughput in vitro drug sensitivity screening applied to primary AML blasts were used to uncover such correlations; however, these methods cannot predict the response of leukemic stem cells (LSCs). Our study aimed to predict in vitro response to targeted therapies, based on molecular markers, with subsequent validation in LSCs. We performed ex vivo sensitivity screening to 46 drugs on 29 primary AML samples at diagnosis or relapse. Using unsupervised hierarchical clustering analysis, we identified group with sensitivity to several tyrosine kinase inhibitors (TKIs), including the multi-TKI, dasatinib, and searched for correlations between dasatinib response, exome sequencing and gene expression from our dataset and from the Beat AML dataset. Unsupervised hierarchical clustering analysis of gene expression resulted in clustering of dasatinib responders and non-responders. In vitro response to dasatinib could be predicted based on gene expression (AUC=0.78). Furthermore, mutations in FLT3/ITD and PTPN11 were enriched in the dasatinib sensitive samples as opposed to mutations in TP53 which were enriched in resistant samples. Based on these results, we selected FLT3/ITD AML samples and injected them to NSG-SGM3 mice. Our results demonstrate that in a subgroup of FLT3/ITD AML (4 out of 9) dasatinib significantly inhibits LSC engraftment. In summary we show that dasatinib has an anti-leukemic effect both on bulk blasts and, more importantly, LSCs from a subset of AML patients that can be identified based on mutational and expression profiles. Our data provide a rational basis for clinical trials of dasatinib in a molecularly selected subset of AML patients.

Bayesian multi-source regression and monocyte-associated gene expression predict BCL-2 inhibitor resistance in acute myeloid leukemia

“…11 and Supplementary Table 10 ). We validated the FLT3 -ITD/GRD association in an independent AML dataset profiling expression and drug response of ex vivo samples published by Tavor and colleagues 14 (one-sided Wilcoxon rank-sum test p < 0.01; Supplementary Fig. 12 ).…”

Expanding dasatinib beyond KIT in acute myeloid leukemia

“…15 In contrast to the molecular focus of dasatinib as an anti-KIT agent in the CBF leukemia studies, Tavor et al identified broader kinase mutations and kinase activity that correlate with dasatinib sensitivity, suggesting that additional biomarkers may be relevant for predicting sensitivity to dasatinib in non-CBF AML. 10 In AML, biomarker-driven personalized medicine is challenged by the therapeutic timeline. Treatment needs to begin quickly once the diagnosis has been made.…”

“…Integration of ex vivo drug sensitivity data and molecular signatures described in Tavor et al10 AUC: area under the curve.…”

“…In this issue, Tavor et al present a focused analysis that leverages careful sample selection with ex vivo drug sensitivity. 10 They applied a 384-well approach to interrogates cell viability in liquid culture after 48 hours assessed across 46 drugs, each at 12 concentrations, which provided a broad area under the curve (AUC) measurement. In this assay, the authors used cytokine combinations (colonystimulating factor, interleukin 3, interleukin 6, thrombopoietin) in liquid culture and avoided stromal cell co-culture to facilitate viability read-out using a streamlined ATP-dependent assay (Cell Titer Glo).…”

“…In contrast to the molecular focus of dasatinib as an anti- KIT agent in the CBF leukemia studies, Tavor et al identified broader kinase mutations and kinase activity that correlate with dasatinib sensitivity, suggesting that additional biomarkers may be relevant for predicting sensitivity to dasatinib in non-CBF AML. 10 …”