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UBC Theses and Dissertations

Characterization of novel therapeutic targets in chronic myeloid leukemia Rothe, Katharina


The identification of BCR-ABL1 as the key molecular event in chronic myeloid leukemia (CML) has revolutionized treatment opportunities for early phase patients. Imatinib mesylate (IM) and other ABL1 tyrosine kinase inhibitors (TKIs) have been introduced into the clinic with remarkable effects. However, initial and acquired resistance, relapse and in particular, the persistence of CML stem cells upon TKI therapy represent critical challenges and warrant the identification of predictive biomarkers and novel, distinct targets for improved treatment strategies. In this work, I investigated how CML stem and progenitor cells survive TKI therapy through intrinsic and bone marrow (BM) niche-associated mechanisms. I revealed that the core autophagy protease ATG4B, and the focal adhesion protein and serine/threonine kinase Integrin-linked kinase (ILK) play crucial roles in CML, and that they can be successfully targeted with small molecule inhibitors. By comparing the expression of various core autophagy genes and proteins, ATG4B was identified as potential biomarker in CML to predict IM-responders versus IM-nonresponders prior to the initiation of therapy. Furthermore, my studies illustrated that deregulation of ATG4B is critical to autophagy, survival and growth of CML stem and progenitor cells. Inhibition or suppression of ATG4B decreased CML cell viability significantly and sensitized leukemic cells to TKI treatment highlighting ATG4B as a novel target in CML. ILK was identified as a differentially expressed gene between CD34⁺ CML patient cells and healthy donors by RNA-sequencing (RNA-seq) analysis, and the importance of the ILK protein and its kinase functions in mediating TKI responses and resistance in CML stem and progenitor cells was demonstrated by ILK inhibitor (QLT0267) and ILK suppression studies. Moreover, various in vitro and in vivo assays showed that the simultaneous kinase inhibition of ILK and BCR-ABL1 is effective in targeting both leukemic stem and progenitor cells, including quiescent CML cells, and in the presence of stromal cells of the BM microenvironment that make TKI monotherapies ineffective. Overall, these studies provide the first evidence of the importance of ATG4B and ILK in CML, and their potential as novel therapeutic targets for improved combination treatments with TKIs to specifically eliminate CML stem and progenitor cells.

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