Abstract 982: Analysis of clonal evolution of leukemia in vivo following novel targeted treatments
Authors: Ojamies Naga Poojitha , Kontro Mika , Edgren Henrik , Eldfors Samuli , Ellonen Pekka , Pemovska Tea , Sonja Langstrom , Almusa Henrikki , Lepisto Maija , Aittokallio Tero , Wennerberg Krister , Heckman Caroline , Porkka Kimmo , Kallioniemi Olli 
Published: May 2015

Acute myeloid leukemia (AML) is a genetically heterogeneous disease characterized by significant clonal evolution. It is critical to understand clonal diversity and evolution during cancer progression and drug resistance in order to tailor curative therapies that block the growth of the multiple AML subclones in each patient.

In our individualized systems medicine (ISM) initiative, we performed ex-vivo drug sensitivity and resistance testing (DSRT) with a comprehensive set of 306 cancer drugs on primary cells from 22 AML patients (Pemovska et al, Cancer Discovery, 2013). Objective clinical responses were seen in 3/6 chemorefractory patients treated based on DSRT results. Here, we applied next-generation genome and transcriptome sequencing in order to a) follow clonal progression of adult AML in patients during treatment with novel targeted drugs, b) identify putative cancer predisposing mutations in patients who later develop aggressive relapsed AML.

Serial samples were obtained from each patient during diagnosis, treatment, remission and relapse. The data indicated significant clonal evolution and emergence of new subclones after relapse and drug resistance. In one such case, treatment of an AML patient with a combination of dasatinib-sunitinib-temsirolimus led to the selection of an already existing low-frequency subclone carrying ETV6-NTRK3 fusion. DSRT of the relapsed sample indicated addiction to IGF1R signalling, compatible with the NTRK3-fusion acting as a driver gene for drug resistance after this treatment. Similar trend where a low-frequency subclone was selected for in the resistance sample was seen in 3 other cases analyzed. Thereby, in depth analysis of clonal evolution from paired AML samples should facilitate the design of new combinatorial regimens to block relapse from arising.

Altogether, we analyzed the genomic profile of 20 recurrent, chemorefractory AML cases. The profile was different between the individual patients and showed an overrepresentation of FLT3 and WT1 mutations, whereas previously reported recurrent mutations in primary AML such as DNMT3A, IDH1/2 and RUNX1 mutations were seen only in individual cases.

We also analyzed the germline variants in the 20 cases, of which two had a positive family history. These patients were analyzed to identify putative variants predisposing these patients to refractory AMLs. The finnish population data comprising of exome sequencing data of 3700 individuals was used to filter the germline variants and assess their potential significance. This analysis indicated recurrent germline changes in multidrug resistance superfamily of genes, which suggests potential germline clues to the etiology to the chemorefractory, recurrent AML cases.

Citation Format: Naga Poojitha Ojamies, Mika Kontro, Henrik Edgren, Samuli Eldfors, Pekka Ellonen, Tea Pemovska, Langstrom Sonja, Henrikki Almusa, Maija Lepisto, Tero Aittokallio, Krister Wennerberg, Caroline Heckman, Kimmo Porkka, Olli Kallioniemi. Analysis of clonal evolution of leukemia in vivo following novel targeted treatments. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 982. doi:10.1158/1538-7445.AM2014-982