Abstract 65: Comprehensive ex vivo drug sensitivity testing combined with in depth molecular profiling of AML patients cells provides individualized treatment strategies and reveals mechanisms of drug resistance.
Authors: Wennerberg Krister , Pemovska Tea , Kontro Mika , Yadav Bhagwan , Kulesskiy Evgeny , Edgren Henrik , Eldfors Samuli , Karjalainen Riikka , Kota Venkata Naga Poojitha , Lehto Anna , Majumder Muntasir Mamun , Malani Disha , Murumägi Astrid , Turunen Laura , Knowles Jonathan , Aittokallio Tero , Heckman Caroline , Porkka Kimmo , Kallioniemi Olli 
Published: August 2014

Acute myeloid leukemia (AML) is an aggressive, heterogeneous disease with few options for targeted therapy. Here, we describe a novel translational strategy termed Individualized Systems Medicine (ISM), in which we profile primary AML patient cells functionally, molecularly and clinically to identify novel treatment strategies for patients, monitor and predict disease progression and follow-up therapies, and elucidate drug response and resistance mechanisms.

We developed a comprehensive ex vivo drug sensitivity and resistance testing (DSRT) strategy to screen AML patient blast cells ex vivo against a set of 202 conventional chemotherapeutic and targeted approved (n=119) and investigational (n=83) drugs. Quantitative leukemia-selective drug sensitivity scores for each drug were determined by comparing the area under the dose response curve from the patient cells to that of healthy control mononuclear cells. Analysis of consecutive samples from the same patients with DSRT and next-generation sequencing was applied to infer clonal evolution and potential mechanisms of drug response and resistance.

Twenty-four samples from 16 recurrent and refractory AML patients were profiled by DSRT, sequencing and proteomic approaches. Several approved and late stage clinical investigated targeted drugs including multi-kinase inhibitors (e.g. dasatinib, sunitinib), TORC1 inhibitors (e.g. temsirolimus), JAK inhibitors (e.g. ruxolitinib) and MEK inhibitors (e.g. trametinib, selumetinib) showed selective leukemic-specific responses in 10-30% of AML samples from patients with recurrent disease. In two refractory AML cases where dasatinib, sunitinib and temsirolimus showed selective responses, the clinical administration of these compounds resulted in complete and partial remission, but was followed by resistance to the applied drugs. Re-sampling and DSRT retesting of cells confirmed diminished sensitivities to the administered drugs, but also indicated new acquired drug sensitivities. Exome and RNA sequencing of the serial samples from both patients revealed diverse subclonal populations characterized by multiple somatic mutations, which were either lost or gained during disease progression and represented drug sensitive or resistant subclones.

In conclusion, our results suggest that an ISM strategy based on consecutive cancer sampling, ex vivo DSRT and analysis of clonal evolution could facilitate the rapid design of improved combinatorial therapies for AML. This strategy can also help tailor optimized therapies for patients, and prioritize introduction of new drugs for clinical testing.

Citation Format: Krister Wennerberg, Tea Pemovska, Mika Kontro, Bhagwan Yadav, Evgeny Kulesskiy, Henrik Edgren, Samuli Eldfors, Riikka Karjalainen, Naga Poojitha Kota Venkata, Anna Lehto, Muntasir Mamun Majumder, Disha Malani, Astrid Murumägi, Laura Turunen, Jonathan Knowles, Tero Aittokallio, Caroline Heckman, Kimmo Porkka, Olli Kallioniemi. Comprehensive ex vivo drug sensitivity testing combined with in depth molecular profiling of AML patients cells provides individualized treatment strategies and reveals mechanisms of drug resistance. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 65. doi:10.1158/1538-7445.AM2013-65