Modeling Resistance To Tyrosine Kinase Inhibitors In TEL/ABL-Positive Acute Lymphoblastic Leukemia
Authors: Zimmermannova Olga , Zuna Jan , Polakova Katerina Machova , Lizcova Libuse , Zemanova Zuzana , Chen I-Ming L. , Falkenburg JH Frederik , Harvey Richard C. , Willman Cheryl L. , Trka Jan , Zaliova Marketa 
Published: October 2019

Abstract
TEL/ABL-positive (TEL/ABL+) acute lymphoblastic leukemia (ALL) is a very rare prognostically unfavorable disease. Its pathogenesis is similar to the BCR/ABL-positive (BCR/ABL+) ALL. TEL/ABL kinase activity can be inhibited by tyrosine kinase inhibitors (TKI), which may be used in the therapy of TEL/ABL+ ALL. Thanks to the rareness of TEL/ABL+ ALL there is a lack of knowledge on potential development of TKI resistance and its mechanisms.
We have used previously established TEL/ABL+ ALL cell line (Baeumler et al., Cancer Genetics and Cytogenetics, 2008) to create a TKI resistant daughter cell line and study the kinetic and mechanism of its resistance. Resistance to IM was acquired after a very long term (16 months) exposure to slowly increasing doses of imatinib mesylate (IM). We have tested the sensitivity of the newly established resistant cell line against a panel of 7 kinase inhibitors and we found that the cell line acquired resistance not only to IM but also to dasatinib, nilotinib and ponatinib, while it remained sensitive to bosutinib, sunitinib and sorafenib. The resistance to IM remained stable even after the withdrawal of IM from the growth medium and was not abrogated by the co-treatment with valproic acid, which has potential to reverse imatinib resistance in BCR/ABL-positive leukemia (Morotti et al., Cancer, 2006). These findings imply that the cells acquired de novo resistance rather than that primarily resistant subclone was selected, and that the acquired resistance has a genetic background.
We have studied several potential mechanism of IM-resistance described in BCR/ABL+ leukemia - mutations in ABL kinase domain, genomic amplification and enhanced expression/autophosphorylation of chimeric protein - but we did not find any of them to be acquired by our resistant cell line. To screen for other potential causes of IM resistance we have performed whole genome genomic profiling by high density SNP arrays, whole genome gene expression profiling and whole exome sequencing. Genomic profiling and subsequent FISH analysis of parental versus resistant cell line revealed 3 discordant aberrations: amplification of 8q24.13-24.3, deletion of 10q26.13-26.3 and deletion of 13q12.12-12.13. Gene expression profiling showed broad changes in expression pattern with at least 2 fold change of expression between parental and resistant cell line in 566 probes representing 469 genes. Interestingly, this 469-gene set contained 5/27 genes from a published gene set which expression correlates with survival in BCR/ABL-positive ALL (Juric et al, Journal of Clinical Oncology, 2007) - the changes in their expression in the resistant versus parental cell line correspond to the changes between the patients with the worse versus better survival. Functional annotation of these 469 differentially expressed genes covers spectrum of diverse biological processes and pathways. Of interest, 2/5 top down-regulated genes in resistant cell line are pro-apoptotic protein PAWR and negative regulator of cytokine signaling SOCS2, both involved in pathways with potential biological relevance for the studied resistance. The data from exome sequencing are currently being analyzed.
To summarize, we have successfully established multi-resistant TEL/ABL+ ALL cell line model to study the kinetics and mechanism of TKI resistance. We have demonstrated a very slow kinetics of the IM-resistance induction and excluded several resistance mechanisms typically found in BCR/ABL+ leukemia such as ABL kinase domain mutations, genomic amplification or enhanced expression/phosphorylation of the chimeric protein. We found 3 genomic and multiple gene expression changes to be associated with the resistant phenotype, their contribution to the mechanism of the resistance will be subjected to future studies.
Grant support: IGA MZ NT/2121167; UNCE 204012; RVO-FNM64203; RVO-VFN64165

Disclosures:
No relevant conflicts of interest to declare.