Ponatinib Resistance Research Articles

A Niche-Based Cell Mutagenesis Assay Identifies ABL-Kinase Mutations Appearing in BCR-ABL T315I-Mutated Leukemic Cells Treated with Ponatinib.

AbstractAbstract 2436The occurrence of ABL-kinase (ABL-K) mutation is a major persisting concern in CML patients treated with tyrosine kinase inhibitor (TKI) therapies. Leukemic stem cell niche can protect the leukemic cells by providing survival and/or quiescence signals but also could favor the occurrence of ABL-kinase mutations. Amongst the ABL-kinase mutations, T315I is one of the most problematic as it induces resistance to all three clinically accepted TKI (Imatinib, Dasatinib, Nilotinib) and has been shown to occur at the level of stem cells (Chomel et al, Leuk lymphoma 2010). Ponatinib (Formerly AP24534) is a multi-targeted TKI which overcomes resistance to T315I mutation as well as to other ABL-kinase mutations. To model the role of the niche in the context of T315I in patients treated with Ponatinib, we designed a niche-based cell mutagenesis assay in the human hematopoietic UT7 cells engineered to express BCR-ABL (UT7-BCR-ABL native cells) and BCR-ABL with T315I (UT7-T315I), via retrovirus mediated gene transfer. Western blot analyses demonstrated that these cells express BCR-ABL and UT7 clones harboring the T315I mutation were resistant to Imatinib, Dasatinib and Nilotinib but sensitive to Ponatinib. We have treated UT7-T315I cells with N-ethyl-N-nitrosourea (ENU, 50microg/ml) for 24 hours and seeded them on previously prepared MS5 stromal cells (plate of 96 wells) in the presence of Ponatinib (30 nM final concentration). As a control, ENU-treated cells were also cultured in the absence of MS5 feeders and Ponatinib-based selection was performed in the same conditions. The same niche-based assay was also performed in the UT7-BCR-ABL native cells and selection process has taken place in the presence of Imatinib (2 microM). Cell medium was changed every week with addition of Ponatinib (UT7-T315I cells) or Imatinib (UT7-BCR-ABL native cells). At week+4, Ponatinib-resistant and IM-resistant wells cultured in the presence (MS5+) or in the absence (MS5-) of the hematopoietic niche were enumerated. In UT7-BCR-ABL native plates, the numbers of IM-resistant outgrowth was identical in MS5+ versus MS5- conditions (51/95 and 54/96, respectively). On the other hand, in UT7-T315I plates, there was a major difference in the numbers of Ponatinib-resistant T315I cells in MS5+ (96/96, 100% survival) as compared to MS5- conditions (65/96, 62 % survival). IM and Ponatinib-resistant clones were amplified and 48 clones resistant to Ponatinib (MS5+ n= 24; MS5- n= 24) and 48 clones resistant to IM (MS5+ n= 24: MS5- n=24) were screened for ABL-K mutations using a denaturing gradient gel electrophoresis assay followed by direct sequencing of the ABL-kinase domain. In the native BCR-ABL mutagenesis assay (with Imatinib), all clones were found mutated, in the presence or absence of MS5 stromal cells. Most of them were mutated in the P-loop region (E255K, G250E, Y253H). In addition, we have found 3 clones harboring the T315I mutation (1 in MS5- and 2 in MS5+ conditions). Concerning T315I clones surviving to Ponatinib, in addition to the T315I mutation, most of the resistant clones harbored an additional P-loop mutation which occrred in the absence or presence of MS5. Moreover, in two clones, two additional mutations were detected in addition to the T315I mutation. Interestingly, when Ponatinib-resistant cells were switched from MS5+ conditions to MS5- conditions, Ponatinib resistance could be abrogated in some but not all cases. In conclusion, our assay shows that the hematopoietic stem cell niche could play a crucial role in conferring resistance to Ponatinib, not only via the occurrence of novel mutations but also by providing survival signals. Preliminary results also suggest that the hematopoietic niche could facilitate the emergence of T315I mutation in cells expressing native BCR-ABL. These results could be important to study the mechanisms of the occurrence and selection of ABL-K mutations in patients treated with TKI including Ponatinib, and to develop niche-targeted therapies to overcome TKI-resistance in CML. Disclosures:Turhan:Novartis, Bristol Myers Squibb: Honoraria, Research Funding.

Partially or Fully BCR-ABL Independent Mechanisms of in Vitro Resistance to Ponatinib

Abstract 2481Ponatinib (AP24534) is a pan-BCR-ABL inhibitor developed for treatment-refractory chronic myeloid leukemia (CML) and has significant activity in patients who fail second-line dasatinib and/or nilotinib tyrosine kinase inhibitor (TKI) therapy. A pivotal phase II trial (clinicaltrials.gov NCT01207440) is underway. BCR-ABL kinase domain mutation-mediated ponatinib resistance has been investigated in vitro (Cancer Cell 16, 2009, 401). Here, we developed ponatinib-resistant, BCR-ABL+ cell lines lacking a kinase domain mutation and investigated mechanisms of resistance to ponatinib and other TKIs. Methods:Four BCR-ABL+ CML cell lines (K562, AR230, BV173, and 32D(BCR-ABL)) were maintained in liquid culture containing ponatinib (0.1 nM) for 10 days. The ponatinib concentration was increased in small increments for a minimum of 90 days, yielding corresponding ponatinib-resistant cell lines. BCR-ABL kinase domain sequencing of sensitive and resistant cells confirmed BCR-ABL to be unmutated. Real-time qPCR was used to compare the expression of BCR-ABL in ponatinib-sensitive and -resistant cell lines. Immunoblot analysis (total and tyrosine-phosphorylated BCR-ABL) was used to the compare levels of BCR-ABL protein and to determine whether resistance to ponatinib corresponded with reduced (partially BCR-ABL-independent) or complete inhibition of BCR-ABL tyrosine phosphorylation (fully BCR-ABL-independent). Cell proliferation assays were performed on resistant and sensitive cell lines in the presence of ponatinib, nilotinib, and dasatinib. A small-molecule inhibitor screen composed of >90 cell-permeable inhibitors that collectively target the majority of the tyrosine kinome as well as other kinases (Blood 116, 2010, abstract 2754) is currently being applied to the 32D(BCR-ABL)R cell line in the presence of 24 nM ponatinib to assess synthetic lethality, with results analyzed using a companion drug sensitivity algorithm. As a second strategy to generate resistant lines, N-ethyl-N-nitrosourea (ENU) mutagenesis was done to investigate BCR-ABL kinase domain-mediated resistance in myeloid K562, AR230, BV173, and 32D(BCR-ABL) cells. After ENU exposure, cells were washed and cultured in 96-well plates with escalating ponatinib. Results:The four BCR-ABL+ cell lines initially grew in the presence of 0.1 nM but not 0.5 nM ponatinib. Upon gradual exposure to escalating ponatinib, each of the cell lines exhibited a degree of adaptation to growth in the presence of the inhibitor (range: 10 to 240-fold). Real-time qPCR showed a modest two-fold increase in BCR-ABL expression level in K562R, AR230R and BV173R cell lines relative to the respective parental lines. Based on immunoblot analysis, cell lines segregated into two categories of ponatinib resistance: partially (K562R and AR230R) or fully BCR-ABL-independent (BV173R and 32D(BCR-ABL)R). Cell proliferation assays showed that ponatinib resistant cell lines also exhibited resistance to nilotinib and dasatinib. The 32D(BCR-ABL)R cell line exhibited a level of ponatinib resistance comparable to that of the Ba/F3 BCR-ABLE255V cell line, which carries the most ponatinib-resistant BCR-ABL mutation. BCR-ABL tyrosine phosphorylation was efficiently blocked by low concentrations of ponatinib (<5 nM) in the 32D(BCR-ABL)R cell line, yet these cells remained viable in the presence of up to 24 nM ponatinib. The effects of providing a second kinase inhibitor along with ponatinib (24 nM) in order to probe for synthetic lethality are under study. Possible involvement of a second, moderately ponatinib-sensitive target is suggested by the sharp ponatinib maximum at 24 nM; even 26 nM ponatinib is toxic to 32D(BCR-ABL)R cells. Thus far, ENU mutagenesis screens in human CML cell lines failed to yield resistant clones and only a few were recovered from the murine 32D(BCR-ABL)R cell line (3/1440 wells; the only BCR-ABL mutant recovered was BCR-ABLL387F). Conclusions:The ponatinib resistant, BCR-ABL+ cell lines described here exhibit either a partially or fully BCR-ABL independent mechanism of resistance. The molecular details of both processes will be reported, with an emphasis on the striking level of resistance (240-fold over starting conditions) exhibited by the 32D(BCR-ABL)R cell line. Our in vitro results indicate that BCR-ABL independent mechanisms may contribute to ponatinib resistance in myeloid CML cells. Disclosures:No relevant conflicts of interest to declare.

Analysis of in Vitro Activity of the Clinically-Active ABL/FLT3 Inhibitor Ponatinib (AP24534) Against AC220-Resistant FLT3-ITD Mutants

Abstract 930 Background:Activating mutations in FLT3 are detected in approximately 30 percent of adult acute myeloid leukemia (AML) cases, most commonly in-tandem duplication (ITD) events. Ponatinib (AP24534) is a potent inhibitor of ABL and FLT3 that has shown clinical activity in CML as well as in a limited experience with FLT3-ITD-positive acute myeloid leukemia (AML) with 2/7 kinase inhibitor-naïve AML patients achieving CRi in a phase I study (Talpaz et al, ASCO 2011, abstract #6518). We recently reported that the FLT3 inhibitor AC220, which has achieved an interim composite CR rate of 43% in a phase II study in relapsed/refractory AML (Cortes, et al, EHA 2011, abstract #1019) is vulnerable to a limited number of resistance-conferring kinase domain mutations in vitro (Smith et al, AACR 2011, abstract #4737). Mutations at 2 of these residues, F691 and D835, have been identified in 9/9 FLT3-ITD+ patients who relapsed after achieving clearance of bone marrow blasts on AC220 (Smith et al, ASH 2011, submitted). Notably, AC220-resistant mutations were found to confer cross-resistance to sorafenib. Given that ponatinib retains activity against a wide range of TKI-resistant BCR-ABL mutants, we sought to test its activity against AC220-resistant mutants. Results:We assessed the activity of ponatinib against highly AC220-resistant FLT3-ITD mutations F691I/L, D835V/Y and Y842C/H. Ponatinib potently suppressed the growth of Ba/F3 cells transformed with native FLT3-ITD with an inhibitory concentration 50 (IC50) of 2 nM. Ba/F3 cells transformed with the “gatekeeper” F691I mutation retained sensitivity to ponatinib at a similar concentration (5 nM). This substitution is analogous to the BCR-ABL T315I mutation, which is clinically sensitive to ponatinib. The remaining AC220-resistant FLT3-ITD mutants, including the gatekeeper F691L substitution, conferred a substantial degree of relative cross-resistance to ponatinib. Mutations at the activation loop residue D835 confer the highest degree of resistance. In an effort to identify other substitutions in FLT3-ITD that are capable of conferring ponatinib resistance in vitro, we employed an in vitro mutagenesis strategy (Azam et al, Cell, 2003) of FLT3-ITD in varying concentrations of ponatinib. In a preliminary analysis, we have identified resistance-causing substitutions at D835, as well as other residues in the FLT3 activation loop including D839 and N841. Interestingly, one of these substitutions, D835N, confers resistance to ponatinib but not to AC220.A molecular analysis of the ponatinib/FLT3 complex based on the crystal structure of ABL/ponatinib was performed and revealed that isoleucine substitution at the FLT3 “gatekeeper” residue (F691I), as with the T315I mutation in Abl, does not creates substantial steric clash with ponatinib. In contrast, the leucine substitution, (F691L), is more bulky than isoleucine and may cause more steric hindrance. In addition, as leucine is more rigid than isoleucine, more energy would be required for the F691L mutation to adopt a conformation compatible with ponatinib binding. As ponatinib binds to the “DFG-out” inactive conformation of FLT3, activation loop mutations such as D835V/Y and Y842C/H likely destabilize the activation loop conformation of FLT3 required for ponatinib binding. Conclusions:Our studies demonstrate that gatekeeper and, in particular, activation loop substitutions in FLT3-ITD, confer a high degree of cross-resistance to the clinically-active FLT3 TKIs described to date. Ponatinib retains in vitro activity against the gatekeeper mutation FLT3-ITD/F691I, which confers a high degree of in vitro resistance to AC220, but leucine substitution at this residue notably confers a higher degree of resistance to ponatinib. Activation loop mutations confer substantial degrees of in vitro cross-resistance to ponatinib and are predicted to confer clinical resistance. Select substitutions at D835 appear to confer selective resistance to ponatinib. Categorization of the spectrum of resistance-conferring mutations may facilitate a more personalized approach toward patients with FLT3-ITD+ AML treated with clinically-active TKI therapy. Disclosures:Off Label Use: Investigational agent ponatinib will be discussed. Zhu:Ariad Pharmaceuticals: Employment. Shah:Ariad: Consultancy, Research Funding; Novartis: Consultancy; Bristol-Myers Squibb: Consultancy, Research Funding.

Efficacy of Ponatinib Against ABL Tyrosine Kinase Inhibitor Resistant Leukemia Cells

Abstract 4413Dasatinib (Sprycel®) and nilotinib (Tasigna®) have each shown superior efficacy as front line treatment for patients with chronic myeloid leukemia (CML)-chronic phase (CP) in comparison with imatinib. Dasatinib and nilotinib are also used for the treatment of CML patients resistant or intolerant to imatinib therapy. However, a substantial number of patients are acquired resistance to nilotinib or dasatinib, the management of CML following the development of ABL tyrosine kinase inhibitor (TKI) resistance remains a challenge. Ponatinib, also known as AP24534, is an oral, the multi-targeted TKI. Ponatinib is currently being investigated in a pivotal phase 2 clinical trial (PACE trial) in patients with resistant or intolerant CML and Philadelphia positive acute lymphoblastic leukemia (Ph+ ALL). However, the molecular and functional consequences of ponatinib against ABL TKI resistant cells are not fully known. In this study, we investigated the ponatinib efficacy by using the BCR-ABL positive cell line, K562 and ABL TKI resistant (K562 imatinib resistant (K562IR), K562 nilotinib resistant (K562NR), K562 dasatinib resistant (K562DR) cells and murine Ba/F3 cell line which was transfected BCR-ABL random mutation, and established the new imatinib and nilotinib resistant Ba/F3 BCR-ABL point mutant (E334V) cells. We first examined the cell proliferation by using resistant cell lines. The proliferation of K562IR and K562 NR and K562DR did not decrease after imatinib (10 μM) or nilotinib (2 μM) or dasatinib (1 μM) treatment compared with parental cell line, K562. The BCR-ABL kinase domain mutation was not found. Point mutant Ba/F3 cell (E334V) was also highly resistant to imatinib (IC50: 15μM) and nilotinib (IC50: 7.5μM). We next examined the intracellular signaling by using these cell lines. Phosphorylation of BCR-ABL and Crk-L was not decreased by ABL TKIs in K562IR, K562NR and Ba/F3 BCR-ABL point mutant cells (E334V). We found the one of src family kinase, Lyn was activated in K562IR and K562NR cells. Co-treatment src kinase inhibitor, PP2 and imatinib or nilotinib significantly reduced the cell proliferation of K562IR and K562NR cells. We also found the phosphorylation of Lyn was reduced and poly (ADP-ribose) polymerase (PARP) was activated. We next examined the efficacy of ponatinib against imatinib and nilotinib resistant cell lines. 72 hours treatment of ponatinib exhibits cell growth inhibition against K562 (IC50: 0.02nM), K562IR (IC50: 15nM), and K562NR (IC50: 3.5nM) cells. We also found the phosphorylation of BCR-ABL, Lyn and Crk-L was reduced and PARP was activated after ponatinib treatment. We next examined the imatinib and nilotinib resistant Ba/F3 cells with point mutant (E334V). We found the cell proliferation was significantly decreased after ponatinib treatment (IC50: 3nM). We also found the phosphorylation of BCR-ABL, Crk-L was reduced and PARP was activated after ponatinib treatment. We next investigated the ponatinib activity against dasatinib resistant cells. We found K562DR cells were highly resistant to ponatinib. IC50 was 400nM. These results suggest that the expression and protein activation signatures identified in this study provide insight into the mechanism of resistance to ABL TKIs. We also demonstrate ponatinib has anti-leukemia effect by reducing ABL and Lyn kinase activity and development of ponatinib resistance and suggests that this information may be of therapeutic relevance. Disclosures:No relevant conflicts of interest to declare.