scholarly journals Stroma-Derived Factors Significantly Impact the Drug Response Profiles of Patient-Derived Primary AML Cells: Implications for Drug Sensitivity Testing

Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. 3505-3505
Author(s):  
Riikka Karjalainen ◽  
Tea Pemovska ◽  
Muntasir Mamun Majumder ◽  
David Tamborero ◽  
Bhagwan Yadav ◽  
...  
Keyword(s):  
Board Of Directors ◽  
Conditioned Medium ◽  
Research Funding ◽  
Drug Testing ◽  
Stromal Cell ◽  
Kinase Inhibitors ◽  
Ex Vivo ◽  
Tumor Stroma ◽  
Advisory Committees ◽  
Equity Ownership

Abstract Background: Bone marrow (BM) microenvironment plays an important role in development of drug resistance in acute myeloid leukemia (AML) by supporting survival of therapy resistant leukemic cells that eventually may lead to disease relapse. Consideration of tumor stroma factors is therefore critically important when assessing the efficacy of drugs in the ex vivo drug testing of primary AML cells. To study the effects of tumor stroma factors on the response of AML patient cells ex vivo to a panel of cancer drugs, we evaluated the effects of stroma-derived conditioned medium (CM) on the sensitivity of genomically defined primary AML cells. Methods: Primary AML cells were isolated by Ficoll gradient separation from BM aspirates or peripheral blood of AML patients (n=13). For drug testing, 303 small molecule inhibitors were plated on 384-well plates in 5 different concentrations over a 10,000-fold concentration range. The stromal-cell conditioned medium (CM) was made by culturing human bone marrow (BM) stromal cell line HS-5 (American Type Culture Collection) in RPMI 1640 medium for 3 days. AML cells were added to the plates in either CM diluted with RPMI 1640 medium (25% CM) or in mononuclear cell medium (MCM, Promocell), which was used as the standard medium comparison. Cell viability was measured after 72 h and dose response curves generated for each drug. Drug sensitivity scores (DSS) were calculated as described previously (Yadav et al, 2014). Phosphorylation profiles of 43 proteins were analyzed with a human phospho-kinase array (R&D Systems). In addition, somatic mutations were identified by exome sequencing using DNA from the leukemia cells and matched skin biopsies, while expressed fusion genes were identified by transcriptome sequencing. Results: AML samples with activating mutations to kinases such as FLT3 or PDGFRB exhibited more sensitive ex vivo drug response profiles, particularly to broad-spectrum kinase inhibitors, compared to samples driven by other types of mutations. When the same AML samples were compared between the two conditions, CM or MCM, the drug sensitivities were different for many classes of drugs (Table 1). In CM, samples typically lost sensitivity to many of the tested drugs, such as topoisomerase II inhibitors, BCL2 inhibitors and several other classes of tyrosine kinase inhibitors (TKIs). The loss of TKI sensitivity in CM was particularly striking in the FLT3 and PDGFRB mutated cases. Cluster analysis of overall drug responses for AML samples tested in MCM resulted in a tight group of most TKIs, reflecting their overlapping target profiles. However, when the analysis was applied to responses from the same cells tested in CM, the TKI grouping was more dispersed. Thus, these results indicate that tyrosine kinase signaling is stringently regulated in standard medium, whereas CM helps to support cell survival resulting in lower responses to a range of TKIs. To test this hypothesis, phosphorylation of 43 different kinases was measured with AML samples incubated in either CM or MCM. CM induced phosphorylation of multiple proteins including p38α, HSP27, Src, Lyn, Hck and STAT6 proving the activation of other signaling pathways. Conclusions: Our dataindicate that stromal cell conditioned medium may have prominent effects on ex vivo drug responses of AML cells. BM factors likely provide survival cues that make primary patient-derived AML cells resistant to several targeted agents, such as topoisomerases and TKIs. This underscores the need to develop drug testing methods that take into account tumor-microenvironment interactions. Disclosures Gjertsen: BerGenBio AS: Membership on an entity's Board of Directors or advisory committees; Boehringer Ingelheim : Equity Ownership, Membership on an entity's Board of Directors or advisory committees; Kinn Therapeutics AS: Equity Ownership. Porkka:Bristol-Myers Squibb: Honoraria, Research Funding; Novartis: Honoraria, Research Funding. Kallioniemi:Medisapiens: Consultancy, Membership on an entity's Board of Directors or advisory committees. Wennerberg:Pfizer: Research Funding. Heckman:Celgene: Research Funding.

Identification of Effective Targeted Drug Combinations Using Functional Ex Vivo Screening of Primary Patient Specimens

Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 865-865 ◽  
Author(s):  
Stephen E Kurtz ◽  
Elie Traer ◽  
Jakki Martinez ◽  
Andrew Park ◽  
Jake Wagner ◽  
...  
Keyword(s):  
Board Of Directors ◽  
Research Funding ◽  
Kinase Inhibitors ◽  
Ex Vivo ◽  
Single Agent ◽  
Hematologic Malignancies ◽  
Drug Combinations ◽  
Advisory Committees ◽  
Heat Map ◽  
Equity Ownership

Abstract Introduction: The intratumoral heterogeneity of Acute Myeloid Leukemia (AML) and other hematologic malignancies presents a challenge in developing effective single-agent targeted treatments. Furthermore, the emergence of genetically heterogeneous subclones leading to relapse suggests that effective therapies associated with discrete genotypes may require drug combinations, each of which modulates distinct pathways. In addition, microenvironmental rescue signals as well as tumor-intrinsic feedback pathways in AML and other hematologic malignancy subsets will necessitate combinatorial therapy approaches. Towards the goal of identifying new therapeutic combinations for AML and other hematologic malignancies, we assessed the sensitivity of primary patient samples to various drug combinations using an ex vivo functional platform. Methods: We have previously screened over 1000 primary patient specimens against a panel of single-agent small-molecule inhibitors. Using these historical drug sensitivity data, we ranked drugs by their IC50, and used these rankings to assemble an initial panel (1) of 44 drug combinations consisting primarily of kinase inhibitors with non-overlapping pathways. Primary patient samples (n = 74) with various hematologic malignancies were assessed for sensitivities to these combinations by culturing cells in the presence of fixed molar concentrations of the drugs over a dose series. Sensitivity was assessed by a viability assay on day 3 using a tetrazolium reagent. IC50 values for samples sensitive to a combination were sorted according to disease type and compared to those for each single agent to derive an index of effectiveness. Based on data from panel 1, we generated a second panel (2) consisting of 44 drug combinations, including new combinations of kinase inhibitors as well as combinations of drugs from different classes, such as bromodomain inhibitors, BH3 mimetics, proteasome inhibitors, IDH1/2 inhibitors coupled with kinase inhibitors. Primary patient samples (n = 78) were assessed for sensitivities to these combinations. Results: The performance of drug combinations across AML, ALL, CLL, CML or other MDS/MPN specimens are displayed in a heat map (Figure 1) representing the sensitivities of each drug combination relative to either of the single agents comprising that combination (the combination IC50 divided by the lowest single agent IC50 is our combination ratio). For each combination, we then compared the combination ratio of each individual specimen to the median combination ratio across all specimens tested, and cases with a combination ratio value less than 20% of the median were considered hypersensitive to that combination. We calculated the percentage of cases that were sensitive to each combination within the diagnostic subsets of AML, ALL, CLL, CML, and MDS/MPN and subsets with the most frequent sensitivity to a drug combination are indicated on the heat map (<20%, dark red; 20-50%, dark pink; 50-80%, light pink; and >80%, white). Combinations of two kinase inhibitors that included the p38MAPK inhibitor, doramapimod, were generally more effective on AML and CLL samples than other diagnostic subsets (panel 1). For CLL sample, combinations including midostaurin and either alisertib, ruxolitinib or sorafenib were particularly effective. Among combinations on panel 2, doramapimod coupled with an apoptosis inducer (ABT-199) exhibited broad efficacy on AML samples. In addition, combinations with the bromodomain inhibitor, JQ1, or the BH3 mimetic, ABT-199, were more broadly effective across diagnostic subsets than many of the kinase-kinase pairs tested. To validate the apparent synergies observed with patient samples, we tested selected combinations on AML-derived cell lines and observed synergies, which were supported with combination indices derived by the Chou-Talalay method. Conclusions: These data suggest that specific drug combinations formed either with two kinase inhibitors or with two compounds from different drug classes are effective in a patient-specific manner with enrichment for certain drug pairs within specific diagnostic subsets. While a secondary evaluation is necessary to validate the initial observation of sensitivity, linking this methodology with genetic attributes for patient samples will identify effective combinations of targeted agents and add therapeutic options for AML treatment. Figure 1. Figure 1. Disclosures Pandya: Microsoft: Employment, Equity Ownership. Bolosky:Microsoft: Employment, Equity Ownership. Druker:Oregon Health & Science University: Patents & Royalties; Henry Stewart Talks: Patents & Royalties; CTI Biosciences: Consultancy, Equity Ownership, Membership on an entity's Board of Directors or advisory committees; Novartis Pharmaceuticals: Research Funding; Aptose Therapeutics, Inc (formerly Lorus): Consultancy, Equity Ownership, Membership on an entity's Board of Directors or advisory committees; McGraw Hill: Patents & Royalties; Leukemia & Lymphoma Society: Membership on an entity's Board of Directors or advisory committees, Research Funding; MolecularMD: Consultancy, Equity Ownership, Membership on an entity's Board of Directors or advisory committees; Roche TCRC, Inc.: Consultancy, Membership on an entity's Board of Directors or advisory committees; Blueprint Medicines: Consultancy, Equity Ownership, Membership on an entity's Board of Directors or advisory committees; Bristol-Myers Squibb: Research Funding; Millipore: Patents & Royalties; AstraZeneca: Consultancy; Oncotide Pharmaceuticals: Research Funding; Cylene Pharmaceuticals: Consultancy, Equity Ownership, Membership on an entity's Board of Directors or advisory committees; Fred Hutchinson Cancer Research Center: Research Funding; ARIAD: Research Funding; Gilead Sciences: Consultancy, Membership on an entity's Board of Directors or advisory committees; Sage Bionetworks: Research Funding. Tyner:Incyte: Research Funding; Janssen Pharmaceuticals: Research Funding; Constellation Pharmaceuticals: Research Funding; Array Biopharma: Research Funding; Aptose Biosciences: Research Funding.

Targeting of JAK/STAT Signaling to Reverse Stroma-Induced Cytoprotection Against BCL2 Antagonist Venetoclax in Acute Myeloid Leukemia

Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 32-32
Author(s):  
Riikka Karjalainen ◽  
Mihaela Popa ◽  
Minxia Liu ◽  
Mika Kontro ◽  
Mireia Mayoral Safont ◽  
...  
Keyword(s):  
Board Of Directors ◽  
Stromal Cells ◽  
Research Funding ◽  
Stromal Cell ◽  
Ex Vivo ◽  
Intrinsic Resistance ◽  
Advisory Committees ◽  
Equity Ownership ◽  
Refractory Aml

Abstract Several promising new, targeted agents are being developed for the treatment of AML. The BH3 mimetic venetoclax (ABT-199) is a specific inhibitor of BCL2, with results from a phase 2 study showing transient activity of venetoclax in relapsed/refractory AML (Konopleva et al, 2014). The bone marrow (BM) microenvironment is known to protect AML cells from drug therapy and we showed earlier that conditioned medium (CM) from BM stromal cells applied to AML patient cells conferred resistance to venetoclax, which could be reversed by the addition of the JAK1/2 inhibitor ruxolitinib (Karjalainen et al, 2015). Here, we investigated the mechanisms mediating the BM stromal cell induced resistance to venetoclax and its reversal by ruxolitinib. To identify the soluble factor(s) contributing to stroma-induced protection of BCL2 inhibition, we analyzed the cytokine content of 1) CM from the human BM stromal cell line HS-5, 2) CM from BM mesenchymal stromal cells (MSCs) isolated from AML patients, 3) supernatants from BM aspirates collected from AML patients, and 4) supernatants from BM aspirates collected from healthy donors. Although expression levels varied, the cytokines detected were similar among the different samples. In HS-5 CM, IL-6, IL-8 and MIP-3α were among the most abundant cytokines. In addition, gene expression analysis showed the receptors for these cytokines were expressed in AML patient samples. IL-6, IL-8 and MIP-3α were added individually to mononuclear cells collected from AML patients, which were then treated with venetoclax. However, none of the cytokines alone could mimic the reduced sensitivity to venetoclax conferred by the HS-5 CM suggesting that stromal cell induced cytoprotection is likely multi-factorial. Next we tested the effect of AML-derived BM MSCs on the ex vivo response of AML patient samples (n=8) to ruxolitinib or venetoclax alone or in combination in a co-culture setting. Apoptosis assays showed negligible effects of ruxolitinib at a concentration of 300 nM, while venetoclax at a dose of 100 nM induced reduction in the percentage of CD34+ AML cells. Co-treatment with venetoclax and ruxolitinib demonstrated synergistic effects in 6 out of 8 samples and significantly reduced the number of CD34+ AML cells. Mechanistic studies showed that ruxolitinib treatment inhibited the BM stromal medium-induced expression of BCL-XL mRNA on AML cells and the drugs in combination down-regulated BCL2, MCL1 and BCL-XL protein expression, which was in correlation with sensitivity to the drugs. To further evaluate the ability of the venetoclax and ruxolitinib combination to eradicate leukemic cells in vivo we used an orthotopic xenograft model of AML. NSG mice were injected with genetically engineered MOLM-13luc cells and after engraftment treated with venetoclax (25 mg/kg, i.p.), ruxolitinib (50 mg/kg BID, p.o) or both and imaged once per week for 4 weeks. At the end of the treatment period bioluminescent imaging showed significantly reduced leukemia burden in the ruxolitinib and venetoclax co-treated mice compared to controls demonstrating superior anti-tumor efficacy than either agent alone (Figure 1). In summary, our data demonstrate that the combined blockade of JAK/STAT and BCL2 pathways with ruxolitinib and ventoclax is synergistic in ex vivo co-culture models and in vivo in an AML mouse model. The addition of ruxolitinib was able to overcome intrinsic resistance to venetoclax by reducing expression of MCL1, a known escape mechanism of BCL2 inhibition. These results support further clinical investigation of this combination, particularly for relapsed/refractory AML. Disclosures Porkka: Novartis: Honoraria, Research Funding; Pfizer: Honoraria, Research Funding; Bristol-Myers Squibb: Honoraria, Research Funding. Wennerberg:Pfizer: Research Funding. Gjertsen:BerGenBio AS: Equity Ownership, Membership on an entity's Board of Directors or advisory committees; Boehringer Ingelheim: Membership on an entity's Board of Directors or advisory committees; Kinn Therapeutics AS: Equity Ownership. Heckman:Celgene: Research Funding; Pfizer: Research Funding.

Blockade of PD-1 in Combination with Dendritic Cell/Myeloma Fusion Cell Vaccination Following Autologous Stem Cell Transplantation Is Well Tolerated, Induces Anti-Tumor Immunity and May Lead to Eradication of Measureable Disease

Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 4218-4218 ◽  
Author(s):  
Jacalyn Rosenblatt ◽  
Irit Avivi ◽  
Noam Binyamini ◽  
Lynne Uhl ◽  
Poorvi Somaiya ◽  
...  
Keyword(s):  
Stem Cell ◽  
Dendritic Cell ◽  
Stem Cell Transplantation ◽  
Board Of Directors ◽  
Research Funding ◽  
Ex Vivo ◽  
Advisory Committees ◽  
Post Transplant ◽  
Fusion Cell ◽  
Equity Ownership

Abstract Autologous stem cell transplantation (ASCT) for multiple myeloma (MM) offers a unique setting to incorporate immunotherapy in an effort to target residual disease. Our group has developed a cancer vaccine in which dendritic cells (DCs) are fused to autologous tumor cells resulting in the presentation of multiple tumor antigens with the capacity to elicit a broad anti-tumor response. A fundamental challenge to developing a more effective tumor vaccine is overcoming the immunosuppressive milieu by which tumor cells evade host immunity. Up-regulation of the PD-1/PDL1 pathway represents a key element contributing to tumor-mediated tolerance, and potentially muting response to vaccination. We are conducting a clinical trial in which patients with MM are treated with an anti-PD1 antibody (Pidilizumab, MDV9300) in combination with a dendritic cell/myeloma fusion cell vaccine following autologous transplantation. 22 patients have been treated with post-transplant immunotherapy. Mean age was 64. MM cells were isolated from bone marrow and were identified by expression of CD38 or CD138. Mean tumor cell yield was 118x106 cells. Adherent mononuclear cells were isolated from leukapheresis collections and cultured with GM-CSF and IL-4 for 5-7 days, then exposed to TNFα for 48-72 hours to generate mature DCs. DCs expressed co-stimulatory (mean CD86 75%) and maturation markers (mean CD83 50%). DC and MM cells were co-cultured with PEG and fusion cells were quantified by determining the percentage of cells that co-express unique DC and myeloma antigens. Mean fusion efficiency was 41% and the mean cell dose generated was 4 x 106 fusion cells. Mean viability of the DC, myeloma, and fusion preparations was 92%, 89%, and 85%, respectively. As a measure of their potency as antigen presenting cells, DC/MM fusions potently stimulate allogeneic T cell proliferation ex-vivo (Mean stimulation index of 1.9, 9.2 and 7.1 for tumor, DC and DC/myeloma fusions respectively, n=21) Post-transplant immunotherapy was initiated after recovery from transplant-related toxicities. Median time from transplant to initiation of post-transplant immunotherapy was 80 days. Patients received 3 doses of Pidilizumab at 6-week intervals. DC/myeloma fusion cells vaccination is administered 1 week before each dose of Pidilizumab. To date, 22 patients have completed vaccinations and Pidilizumab. Adverse events judged to be potentially treatment related included grade 1-2 diarrhea, arthralgias, myalgias, fatigue, headache, nausea, chills, transaminitis, cytopenia, elevated TSH, and vaccine site reactions. A significant increase in circulatingtumor reactive lymphocytes was noted following post-transplant immunotherapy, as determined by T cell expressionof IFN-γ by CD8 cells following ex-vivo co-culture withautologous myeloma cell lysate. Mean percentage of tumor reactiveCD8 cells increased from 1.8% post-transplant to a peak of 9.16% following immunotherapy. In the post-transplant period, regulatory T cells fell to minimal levels and remained low throughout the period of immunotherapy. 6 patients achieved a best response of VGPR, 6 patients have achieved a nCR/CR, including 3 who converted to CR following immunotherapy. Median PFS from transplant is 19 months with ongoing follow up. In summary, DC/MM fusion cell vaccination in conjunction with PD1 blockade following ASCT was well tolerated, potently induced anti-tumor immunity, and in a subset of patients, resulted in the eradication of post-transplant measurable disease. Disclosures Richardson: Gentium S.p.A.: Membership on an entity's Board of Directors or advisory committees, Research Funding; Jazz Pharmaceuticals: Membership on an entity's Board of Directors or advisory committees, Research Funding; Millennium Takeda: Membership on an entity's Board of Directors or advisory committees; Novartis: Membership on an entity's Board of Directors or advisory committees; Celgene Corporation: Membership on an entity's Board of Directors or advisory committees. Laubach:Novartis: Research Funding; Onyx: Research Funding; Celgene: Research Funding; Millennium: Research Funding. Anderson:Celgene: Consultancy; Millennium: Consultancy; BMS: Consultancy; Gilead: Consultancy; Oncopep: Equity Ownership; Acetylon: Equity Ownership. Rowe:BioSight Ltd.: Consultancy, Membership on an entity's Board of Directors or advisory committees; Amgen: Consultancy; BioLineRx Ltd.: Consultancy. Kufe:Genus Oncology: Consultancy, Equity Ownership.

Inhibition of USP10 Induces Degradation of Oncogenic FLT3: A Novel Approach to Therapy of Leukemia

Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 524-524
Author(s):  
Sara Buhrlage ◽  
Ellen Weisberg ◽  
Nathan Schauer ◽  
Jing Yang ◽  
Ilaria Lamberto ◽  
...  
Keyword(s):  
Board Of Directors ◽  
Research Funding ◽  
Kinase Inhibitors ◽  
Kinase Inhibitor ◽  
Leukemia Cell ◽  
Initial Assessment ◽  
Large Trial ◽  
Newly Diagnosed ◽  
Advisory Committees ◽  
Equity Ownership

Abstract Acute myeloid leukemia (AML) is the most common type of acute leukemia in adults. Overall, the survival with current chemotherapy is only 20-40%, declining steadily with advancing age. Approximately 30% of AML patients have mutations that constitutively activate the FLT3 gene. The most common FLT3 mutation results in tandem duplications within the juxtamembrane domain, observed in 20-25% of AML patients (internal tandem duplication, ITD), associated with markedly decreased survival. FLT3 kinase domain inhibitors, including SU11248, SU5416, CEP-701 and PKC412 (midostaurin), have been shown to induce partial, and usually brief, remissions in clinical trials of relapsed AML patients when administered as single agents. In a large trial in newly diagnosed patients, however, midostaurin was shown to increase survival when combined with standard chemotherapy.[1] This study supports the notion that inhibition of FLT3 may be important, at least in patients with mutations in the FLT3 gene. Since drug resistance develops in some patients with newly diagnosed AML and virtually all patients with advanced disease, additional strategies to target FLT3 would be of value. We discovered that the deubiquitinating enzyme (DUB) ubiquitin specific protease 10 (USP10) removes a degradative ubiquitin tag from mutant FLT3 thereby contributing to high levels of the oncogenic protein in AML (Fig 1a). Screening of our preclinical DUB inhibitor library for ability to selectively kill growth factor-independent FLT3-ITD-positive Ba/F3 cells over IL-3-dependent parental Ba/F3 cells identified HBX19818, a reported USP7 inhibitor, as the top hit. The effects are not unique to the Ba/F3 system: when profiled against a panel of 7 leukemia cell lines, HBX19818 conferred a substantial growth suppressive effect only to those expressing the FLT3-ITD oncoprotein (Fig 1b). As an initial assessment of the mechanism of HBX19818 we confirmed that it does promote ubiquitin-mediated degradation of FLT3-ITD (Fig 1c) and that the effect is selective as HBX19818 does not impact protein levels of wt FLT3. HBX19818 is published as an irreversible USP7 inhibitor,[2] however DUBome selectivity profiling data we generated identifies USP10 as the most potently inhibited DUB of the compound (USP10 IC50 = 14 µM). We went on to validate USP10 as the DUB that stabilizes FLT3-ITD using a combination of small molecule and genetic experiments. Notably, HBX19818 binds and inhibits USP10 in cells (data not shown), small hairpin knockdown of USP10 phenocopies the antiproliferative and FLT3 degradation effects of HBX19818 (Figure 1d and data not shown), and a direct interaction between USP10 and FLT3-ITD is observed in co-immunoprecipitation experiments (Fig 1e). Additionally, SAR studies reveal correlation among USP10 IC50, FLT3-ITD degradation and anti-proliferative effects for the HBX19818 chemical series, and we identified a second chemotype that phenocopies its effects. In support of the translational potential of USP10 inhibition for FLT3 mutant AML, we observed that both USP10 inhibitor series synergize with FLT3 kinase inhibitors, suppress growth of mutant FLT3-expressing primary AML cells and primagraft AML cells and, importantly, display the ability to overcome the FLT3 inhibitor-resistant mutant FLT3-ITD-F691L among other FLT3 kinase inhibitor-resistant mutants (Fig. 1f and data not shown). Overall, our data strongly support degradation of mutant FLT3 as an alternative approach to therapeutically target FLT3. This approach, which focuses on targeting USP10, could prove more efficacious than kinase inhibitors by simultaneously blocking both enzymatic and scaffolding functions of FLT3, and blocking compensatory increases in FLT3 protein or resistant point mutations associated with some kinase inhibitors. Importantly, this is the first demonstration of stabilization of an AML mutant driver protein by a DUB enzyme and introduces a novel therapy for FLT3 mutant-positive AML. References: 1. Stone, R.M., ASH, 2015. 2. Reverdy, C., et al., Chem Biol, 2012. 19, 467-77. Figure 1. Figure 1. Disclosures Weisberg: novartis: Research Funding. Weinstock:Novartis: Consultancy, Research Funding. Stone:Celator: Consultancy; Pfizer: Consultancy; Xenetic Biosciences: Consultancy; Novartis: Consultancy; Seattle Genetics: Consultancy; Roche: Consultancy; Amgen: Consultancy; ONO: Consultancy; Xenetic Biosciences: Consultancy; Sunesis Pharmaceuticals: Consultancy; Juno Therapeutics: Consultancy; Sunesis Pharmaceuticals: Consultancy; Karyopharm: Consultancy; Celgene: Consultancy, Membership on an entity's Board of Directors or advisory committees; Merck: Consultancy; Abbvie: Consultancy, Membership on an entity's Board of Directors or advisory committees; Seattle Genetics: Consultancy; Agios: Consultancy; Jansen: Consultancy. Gray:Gatekeeper: Equity Ownership; Petra: Consultancy, Equity Ownership; C4: Consultancy, Equity Ownership; Syros: Consultancy, Equity Ownership. Griffin:Janssen: Research Funding; Novartis: Consultancy, Research Funding.

scholarly journals Comparative Analysis of Independent Ex Vivo functional Drug Screens Identifies Predictive Biomarkers of BCL-2 Inhibitor Response in AML

Blood ◽  
2018 ◽  
Vol 132 (Supplement 1) ◽  
pp. 2763-2763 ◽  
Author(s):  
Brian S. White ◽  
Suleiman A. Khan ◽  
Muhammad Ammad-ud-din ◽  
Swapnil Potdar ◽  
Mike J Mason ◽  
...  
Keyword(s):  
Gene Expression ◽  
Board Of Directors ◽  
Research Funding ◽  
Drug Response ◽  
Ex Vivo ◽  
Predictive Performance ◽  
Data Sets ◽  
Advisory Committees ◽  
Data Set ◽  
Equity Ownership

Abstract Introduction: Therapeutic options for patients with AML were recently expanded with FDA approval of four drugs in 2017. As their efficacy is limited in some patient subpopulations and relapse ultimately ensues, there remains an urgent need for additional treatment options tailored to well-defined patient subpopulations to achieve durable responses. Two comprehensive profiling efforts were launched to address this need-the multi-center Beat AML initiative, led by the Oregon Health & Science University (OHSU) and the AML Individualized Systems Medicine program at the Institute for Molecular Medicine Finland (FIMM). Methods: We performed a comparative analysis of the two large-scale data sets in which patient samples were subjected to whole-exome sequencing, RNA-seq, and ex vivo functional drug sensitivity screens: OHSU (121 patients and 160 drugs) and FIMM (39 patients and 480 drugs). We predicted ex vivo drug response [quantified as area under the dose-response curve (AUC)] using gene expression signatures selected with standard regression and a novel Bayesian model designed to analyze multiple data sets simultaneously. We restricted analysis to the 95 drugs in common between the two data sets. Results: The ex vivo responses (AUCs) of most drugs were positively correlated (OHSU: median Pearson correlation r across all pairwise drug comparisons=0.27; FIMM: median r=0.33). Consistently, a samples's ex vivo response to an individual drug was often correlated with the patient's Average ex vivo Drug Sensitivity (ADS), i.e., the average response across the 95 drugs (OHSU: median r across 95 drugs=0.41; FIMM: median r=0.58). Patients with a complete response to standard induction therapy had a higher ADS than those that were refractory (p=0.01). Further, patients whose ADS was in the top quartile had improved overall survival relative to those having an ADS in the bottom quartile (p<0.05). Standard regression models (LASSO and Ridge) trained on ADS and gene expression in the OHSU data set had improved ex vivo response prediction performance as assessed in the independent FIMM validation data set relative to those trained on gene expression alone (LASSO: p=2.9x10-4; Ridge: p=4.4x10-3). Overall, ex vivo drug response was relatively well predicted (LASSO: mean r across 95 drugs=0.62; Ridge: mean r=0.62). The BCL-2 inhibitor venetoclax was the only drug whose response was negatively correlated with ADS in both data sets. We hypothesized that, whereas the predictive performance of many other drugs was likely dependent on ADS, the predictive performance of venetoclax (LASSO: r=0.53, p=0.01; Ridge: r=0.63, p=1.3x10-3) reflected specific gene expression biomarkers. To identify biomarkers associated with venetoclax sensitivity, we developed an integrative Bayesian machine learning method that jointly modeled both data sets, revealing several candidate biomarkers positively (BCL2 and FLT3) or negatively (CD14, MAFB, and LRP1) correlated with venetoclax response. We assessed these biomarkers in an independent data set that profiled ex vivo response to the BCL-2/BCL-XL inhibitor navitoclax in 29 AML patients (Lee et al.). All five biomarkers were validated in the Lee data set (Fig 1). Conclusions: The two independent ex vivo functional screens were highly concordant, demonstrating the reproducibility of the assays and the opportunity for their use in the clinic. Joint analysis of the two data sets robustly identified biomarkers of drug response for BCL-2 inhibitors. Two of these biomarkers, BCL2 and the previously-reported CD14, serve as positive controls credentialing our approach. CD14, MAFB, and LRP1 are involved in monocyte differentiation. The inverse correlation of their expression with venetoclax and navitoclax response is consistent with prior reports showing that monocytic cells are resistant to BCL-2 inhibition (Kuusanmäki et al.). These biomarker panels may enable better selection of patient populations likely to respond to BCL-2 inhibition than would any one biomarker in isolation. References: Kuusanmäki et al. (2017) Single-Cell Drug Profiling Reveals Maturation Stage-Dependent Drug Responses in AML, Blood 130:3821 Lee et al. (2018) A machine learning approach to integrate big data for precision medicine in acute myeloid leukemia, Nat Commun 9:42 Disclosures Druker: Cepheid: Consultancy, Membership on an entity's Board of Directors or advisory committees; ALLCRON: Consultancy, Membership on an entity's Board of Directors or advisory committees; Fred Hutchinson Cancer Research Center: Research Funding; Celgene: Consultancy; Vivid Biosciences: Membership on an entity's Board of Directors or advisory committees; Aileron Therapeutics: Consultancy; Third Coast Therapeutics: Membership on an entity's Board of Directors or advisory committees; Oregon Health & Science University: Patents & Royalties; Patient True Talk: Consultancy; Millipore: Patents & Royalties; Monojul: Consultancy; Gilead Sciences: Consultancy, Membership on an entity's Board of Directors or advisory committees; Amgen: Membership on an entity's Board of Directors or advisory committees; Leukemia & Lymphoma Society: Membership on an entity's Board of Directors or advisory committees, Research Funding; GRAIL: Consultancy, Membership on an entity's Board of Directors or advisory committees; Beta Cat: Membership on an entity's Board of Directors or advisory committees; MolecularMD: Consultancy, Equity Ownership, Membership on an entity's Board of Directors or advisory committees; Henry Stewart Talks: Patents & Royalties; Bristol-Meyers Squibb: Research Funding; Blueprint Medicines: Consultancy, Equity Ownership, Membership on an entity's Board of Directors or advisory committees; Aptose Therapeutics: Consultancy, Equity Ownership, Membership on an entity's Board of Directors or advisory committees; McGraw Hill: Patents & Royalties; ARIAD: Research Funding; Novartis Pharmaceuticals: Research Funding. Heckman:Orion Pharma: Research Funding; Novartis: Research Funding; Celgene: Research Funding. Porkka:Novartis: Honoraria, Research Funding; Celgene: Honoraria, Research Funding. Tyner:AstraZeneca: Research Funding; Incyte: Research Funding; Janssen: Research Funding; Leap Oncology: Equity Ownership; Seattle Genetics: Research Funding; Syros: Research Funding; Takeda: Research Funding; Gilead: Research Funding; Genentech: Research Funding; Aptose: Research Funding; Agios: Research Funding. Aittokallio:Novartis: Research Funding. Wennerberg:Novartis: Research Funding.

scholarly journals Colony Stimulating Factor 1 Receptor (CSF1R) As a Potential Novel Therapeutic Target in CLL

Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 4439-4439
Author(s):  
Tyler Sweeney ◽  
Stephen E Spurgeon ◽  
Jeffrey W. Tyner ◽  
Anupriya Agarwal ◽  
Hibery Ho ◽  
...  
Keyword(s):  
Cell Viability ◽  
Board Of Directors ◽  
Solid Tumor ◽  
Therapeutic Target ◽  
Research Funding ◽  
Ex Vivo ◽  
Advisory Committees ◽  
Equity Ownership ◽  
The Impact ◽  
Macrophage Lineage

Abstract Introduction: Monocyte/macrophage lineage cells have been reported to provide a supportive signal in a variety of neoplastic settings. Tumor-associated macrophages (TAMs) have been shown to provide microenvironmental support that maintains tumor cell viability and growth for a variety of solid tumor types, and these TAMs have been shown to depend on the receptor tyrosine kinase, CSF1R (M-CSFR). Monocyte/macrophage lineage cells have also been implicated in the microenvironment of CLL and are termed nurse-like cells in this setting. However, the role of CSF1R in CLL including potential maintenance of these nurse-like cells has not been explored. Using an ex vivo, functional screening platform applied directly to primary specimens from CLL patients, we have identified recurrent sensitivity to CSF1R inhibitors as well as decreased viability after depletion of CSF1R-expressing monocytes, thereby depriving the CLL cells of an important, microenvironmental growth/survival signal. We also have seen synergistic anti-tumor activity when combining CSF1R inhibitors with idelaisib and ibrutinib which inhibit b-cell receptor (BCR) activated pathways. Methods: We evaluated the impact on cell viability of hundreds of CLL patient specimens against panels of targeted small molecule inhibitors. These panels include two small-molecules with exquisite specificity for CSF1R (GW-2580; ARRY-382). In addition, we evaluated the impact of antibody depletion of monocytes (CD14-depletion) on ex vivo CLL cell viability as well as the effect of monocyte cell depletion on response to CSF1R inhibitors. We also evaluated the combination of GW-2580 or ARRY-382 with idelalisib (PI3kδ inhibitor) and ibrutinib (BTK inhibitor). Results: We found that 20-30% of CLL specimens showed sensitivity to inhibition of CSF1R with good concordance between GW-2580 and ARRY-382. Analysis of clinical and demographic features of these patients failed to reveal correlation of CSF1R with any prominent disease subsets. Flow cytometry analysis revealed that CSF1R was not expressed on CLL cells but only on a subpopulation of CD14-expressing monocytes. Depletion of these monocytes with CD14 antibody had little to no impact on samples not exhibiting ex vivo sensitivity to CSF1R inhibitors, however, samples showing strong sensitivity to CSF1R inhibitors were also quite sensitive to depletion of this CD14-positive monocyte population. After CD14 depletion, the remaining CLL cells showed no further sensitivity to CSF1R inhibitors. Finally, when combined with ibrutinib or idelalisib synergy was seen. Conclusions: These results show that CSF1R is a potential therapeutic target in CLL and suggest that CLL supporting monocytes (nurse-like cells) express CSF1R and depend on CSF1R for viability in a similar manner as TAMs depend on CSF1R in a variety of solid tumor settings. As such, CSF1R inhibitors may deprive CLL cells of this supportive microenvironmental signal resulting in CLL cell death. Therefore, we propose that CSF1R inhibitors, such as ARRY-382, possibly in combination with ibrutinib, idelalisib, or other approved agents, may be a promising new line of therapy to target CLL cells by impacting the tumor microenvironment. Disclosures Spurgeon: Genentech: Honoraria; Acerta Pharma: Research Funding; Bristol Meyers Squibb: Research Funding; Gilead sciences: Honoraria, Research Funding; Janssen: Research Funding; Pharmacyclics: Honoraria. Tyner:Janssen Pharmaceuticals: Research Funding; Incyte: Research Funding; Aptose Biosciences: Research Funding; Constellation Pharmaceuticals: Research Funding; Array Biopharma: Research Funding. Agarwal:CTI BioPharma: Research Funding. Lee:Array Biopharma: Employment. Chantry:Array Biopharma: Employment. Druker:Fred Hutchinson Cancer Research Center: Research Funding; Bristol-Myers Squibb: Research Funding; Henry Stewart Talks: Patents & Royalties; Millipore: Patents & Royalties; Sage Bionetworks: Research Funding; MolecularMD: Consultancy, Equity Ownership, Membership on an entity's Board of Directors or advisory committees; Gilead Sciences: Consultancy, Membership on an entity's Board of Directors or advisory committees; Cylene Pharmaceuticals: Consultancy, Equity Ownership, Membership on an entity's Board of Directors or advisory committees; AstraZeneca: Consultancy; Novartis Pharmaceuticals: Research Funding; Blueprint Medicines: Consultancy, Equity Ownership, Membership on an entity's Board of Directors or advisory committees; Oregon Health & Science University: Patents & Royalties; CTI Biosciences: Consultancy, Equity Ownership, Membership on an entity's Board of Directors or advisory committees; Leukemia & Lymphoma Society: Membership on an entity's Board of Directors or advisory committees, Research Funding; Oncotide Pharmaceuticals: Research Funding; Roche TCRC, Inc.: Consultancy, Membership on an entity's Board of Directors or advisory committees; McGraw Hill: Patents & Royalties; ARIAD: Research Funding; Aptose Therapeutics, Inc (formerly Lorus): Consultancy, Equity Ownership, Membership on an entity's Board of Directors or advisory committees.

scholarly journals T-Cell Suppression By Src/ABL Kinase Inhibitors When Combined with Blinatumomab in Ph+ Acute Lymphoblastic Leukemia

Blood ◽  
2018 ◽  
Vol 132 (Supplement 1) ◽  
pp. 2694-2694 ◽  
Author(s):  
Jessica Leonard ◽  
Yoko Kosaka ◽  
Pavani Malla ◽  
Brandon Hayes-Lattin ◽  
Adam J. Lamble ◽  
...  
Keyword(s):  
T Cell ◽  
Board Of Directors ◽  
Research Funding ◽  
Kinase Inhibitors ◽  
Cell Function ◽  
Lymphoblastic Leukemia ◽  
Advisory Committees ◽  
Abl Kinase ◽  
Equity Ownership ◽  
Abl Kinase Inhibitors

Abstract Introduction: Targeted ABL kinase inhibitors (TKIs) have shown great activity in Ph+ Acute Lymphoblastic Leukemia (Ph+ ALL), however relapsed disease remains an unmet need. The bispecific antibody blinatumomab was recently approved as a single agent for use in patients with Ph+ ALL and there is much interest in combining this with targeted therapies. Second generation ABL kinase inhibitors inhibit both Src and LYN in addition to ABL. This is of particular interest in Ph+ ALL as LYN is important for leukemogenesis. T cell receptor (TCR) signaling is also dependent upon Src family kinase activity, and Src inhibitors may impact the efficacy of immunotherapies reliant on native T cell function. We sought to investigate the in vitro effects of ABL specific vs dual Src/ABL kinases on blinatumomab efficacy in both healthy donor as well as primary patient samples. Methods: We isolated peripheral blood mononuclear cells (PBMC) via Ficoll-Hypaque gradient from five healthy donors as well as from two patients with de novo and one patient with relapsed Ph+ ALL who harbored a T315I mutation. PBMC were labeled with CellTrace Violet and cultured for 5 days with no stimulation, blinatumomab, or blinatumomab in combination with imatinib, dasatinib, ponatinib or nilotinib at varying concentrations. Immunophenotyping was performed using multi-parameter flow cytometry for the following cell surface markers: CD45, CD3, CD4, CD8, CD56, and CD19. Blinatumomab efficacy was assessed by comparing the numbers of CD19+ / CD3- cells in untreated samples to those that had been treated with blinatumomab in the presence or absence of TKIs. Cell division of T cells was measured by CellTrace Violet dilution. Cytokine production was assessed via LEGENDplex Human Th Cytokine Panel. Levels of total Src, phospho-Src, total LCK and phospho-LCK were assessed via immunoblot. Results: After 5 days of exposure, blinatumomab led to T-cell proliferation in both healthy donor and patient PBMCs. Proliferation was observed in both CD8+ and CD4+ T cell subsets, although the effect was more pronounced in CD8+ cells. T cell proliferation, however, was completely suppressed by either dasatinib or ponatinib at nanomolar concentrations. This effect was far less pronounced with the ABL kinase inhibitors imatinib and nilotinib. Treatment of PBMCs with blinatumomab led to increased production of the cytokines IFN-g, IL-17-a and IL-22 in patient samples and healthy donors, while levels of IL-6 were increased in the patient samples only and levels of IL-10 in healthy subjects only. Cytokine production was absent in samples treated with blinatumomab and either dasatinib or ponatinib, while levels of IFN-g, IL-17a and IL-22 were minimally affected when blinatumomab was combined with imatinib. Immunoblots confirmed that dasatinib and ponatinib but not imatinib nor nilotinib inhibited phosphorylation of total Src as well as of LCK, likely explaining the inhibitory effects of these agents. In patient samples, blinatumomab alone and the TKIs alone greatly reduced the number of CD19+ cells. However, when dasatinib and blinatumomab were combined in the sample with a T315I mutation, there was little reduction in the percentage of CD19+ cells and no amplification of CD3+ cells, suggesting that dasatinib was able to inhibit the cytotoxic effects of blinatumomab with no effect to the leukemic cells. Discussion: Our results suggest that the combination of dual Src/ABL inhibitors with blinatumomab may abrogate the effects of blinatumomab by directly inhibiting T cell function. This is likely via inhibition of LCK, a known member of the TCR signaling pathway. Although small case series have reported responses in patients treated with blinatumomab and TKIs, it is possible that the majority of the response is from the TKI rather than blinatumomab. Only a randomized trial of a TKI +/- blinatumomab would be able to discern whether there is benefit of adding a dual Src/ABL TKI to bispecific antibody therapy. While our data are limited by sample numbers and by the fact that responses in living subjects may differ according to many other complex interactions in the in vivo immune microenvironment, the potential immunomodulatory effects of targeted therapies should be taken into consideration before they are combined with immunotherapies. Disclosures Leonard: Amgen: Research Funding. Druker:McGraw Hill: Patents & Royalties; Fred Hutchinson Cancer Research Center: Research Funding; Amgen: Membership on an entity's Board of Directors or advisory committees; ARIAD: Research Funding; Monojul: Consultancy; Millipore: Patents & Royalties; Novartis Pharmaceuticals: Research Funding; Oregon Health & Science University: Patents & Royalties; Leukemia & Lymphoma Society: Membership on an entity's Board of Directors or advisory committees, Research Funding; Bristol-Meyers Squibb: Research Funding; ALLCRON: Consultancy, Membership on an entity's Board of Directors or advisory committees; Celgene: Consultancy; Gilead Sciences: Consultancy, Membership on an entity's Board of Directors or advisory committees; Blueprint Medicines: Consultancy, Equity Ownership, Membership on an entity's Board of Directors or advisory committees; Cepheid: Consultancy, Membership on an entity's Board of Directors or advisory committees; Beta Cat: Membership on an entity's Board of Directors or advisory committees; MolecularMD: Consultancy, Equity Ownership, Membership on an entity's Board of Directors or advisory committees; Patient True Talk: Consultancy; Vivid Biosciences: Membership on an entity's Board of Directors or advisory committees; Third Coast Therapeutics: Membership on an entity's Board of Directors or advisory committees; GRAIL: Consultancy, Membership on an entity's Board of Directors or advisory committees; Aileron Therapeutics: Consultancy; Henry Stewart Talks: Patents & Royalties; Aptose Therapeutics: Consultancy, Equity Ownership, Membership on an entity's Board of Directors or advisory committees. Tyner:Constellation: Research Funding; Vivid Biosciences: Membership on an entity's Board of Directors or advisory committees; Janssen: Research Funding; Gilead: Research Funding; Aptose: Research Funding; Incyte: Research Funding; Genentech: Research Funding; Array: Research Funding; Takeda: Research Funding; AstraZeneca: Research Funding. Lind:Celgene: Research Funding; Janssen Pharmaceutical R&D: Research Funding; Amgen: Research Funding; Fluidigm: Honoraria; Monojul: Research Funding.

scholarly journals Comparative Efficacy Among 3rd Line Post-Imatinib Chronic Phase-Chronic Myeloid Leukemia (CP-CML) Patients after Failure of Dasatinib or Nilotinib Tyrosine Kinase Inhibitors

Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. 4551-4551 ◽  
Author(s):  
Jeffrey H. Lipton ◽  
Dhvani Shah ◽  
Vanita Tongbram ◽  
Manpreet K Sidhu ◽  
Hui Huang ◽  
...  
Keyword(s):  
Chronic Myeloid Leukemia ◽  
Board Of Directors ◽  
Myeloid Leukemia ◽  
Research Funding ◽  
Kinase Inhibitors ◽  
Cytogenetic Response ◽  
Comparative Efficacy ◽  
Employment Equity ◽  
Advisory Committees ◽  
Equity Ownership

Abstract INTRODUCTION Patients with chronic myeloid leukemia (CP-CML) failing 1st line imatinib are most commonly treated with the second-generation (2G) tyrosine kinase inhibitors (TKIs) dasatinib and nilotinib. However, for patients who experience resistance or intolerance (R/I) to 2G-TKIs in 2nd line, there currently is no consensus on the optimal therapy sequence for 3rd line treatment. The comparative efficacy of using ponatinib in the 3rd line after 2G TKI failure was examined in a previous study (Lipton et al., ASH 2013). This study assesses the comparative efficacy of ponatinib versus sequential treatment of alternate 2G TKIs in 3rdline setting in two separate patient populations, post-imatinib and dasatinib patients and post-imatinib and nilotinib patients. METHODS A systematic review was conducted in MEDLINE, EMBASE and the Cochrane Libraries (2002-2014), as well as 3 conferences (ASH (2008-2014), ASCO (2008-2014), and EHA (2008-2013)). Studies evaluating any TKI were included if they enrolled 10 or more post-imatinib adult patients with CP-CML who were also R/I to dasatinib or nilotinib. All study designs were considered and no restriction was applied with respect to therapy dose, due to incomplete reporting of doses in the available studies. Analyses was run on two groups of patients, those failing imatinib and dasatinib (Group Ima/Das) and those failing imatinib and nilotinib (Group Ima/Nil). Bayesian methods were used to synthesize major cytogenetic response (MCyR) and complete cytogenetic response (CCyR) from individual studies and estimate the overall response probability with 95% credible interval (CrI) for each treatment. Bayesian analysis also was used to estimate the likelihood that each treatment offers the highest probability of CCyR/MCyR based on available evidence. RESULTS Six studies evaluating bosutinib, nilotinib and ponatinib for Group Ima/Das (n= 419) and five studies evaluating bosutinib, dasatinib and ponatinib for Group Ima/Nil (n=83) were included in the analysis. All studies reported CCyR in both groups. Five studies evaluating bosutinib, nilotinib and ponatinib reported MCyR in Group Ima/Das and three studies evaluating bosutinib and ponatinib reported MCyR in Group Ima/Nil. Synthesized treatment-specific probabilities and 95% CrI for CCyR are presented in Figure 1. Synthesized treatment-specific probabilities of CCyR for Group Ima/Das were 27% for nilotinib, 20% for bosutinib and 54% (95% CrI 43%% to 66%) for ponatinib. Treatment-specific probabilities of MCyR for Group Ima/Das were 41% for nilotinib, 28% for bosutinib and 66% (95% CrI 55%% to 77%) for ponatinib. The probability of ponatinib providing superior response to all other included treatments for group Ima/Das was estimated to be >99% for both CCyR and MCyR. Synthesized treatment-specific probabilities of CCyR for Group Ima/Nil were 25% for dasatinib, 26% for bosutinib and 67% (95% CrI 51%% to 81%) for ponatinib. Treatment-specific probabilities of MCyR for Group Ima/Nil were 33% for bosutinib and 75% (95% CrI 60%% to 87%) for ponatinib. The probability of ponatinib providing superior response to all other included treatments for group Ima/Nil was estimated to be >99% for both CCyR and MCyR. CONCLUSIONS The post imatinib and dasatinib group included more studies with larger sample sizes compared with the post imatinib and nilotinib group. Overall, response rates appear higher for TKIs in the post imatinib and nilotinib group compared with the post imatinib and dasatinib group. For both groups, patients on ponatinib had higher CCyR and MCyR rates compared with the sequential 2G TKIs included in this analysis. Based on available data, ponatinib appears to provide a higher probability of treatment response for patients failing imatinib and dasatinib/ nilotinib compared with sequential 2G TKI therapy commonly used in this indication. Figure 1 Figure 1. Disclosures Lipton: Novartis: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau; Bristol Myers: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau; Ariad: Equity Ownership, Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau; Pfizer: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau. Shah:Ariad Pharmaceuticals: Research Funding. Tongbram:Ariad Pharmaceuticals: Research Funding. Sidhu:Ariad Pharmaceuticals Inc.: Research Funding. Huang:ARIAD Pharmaceuticals, Inc.: Employment, Equity Ownership. McGarry:ARIAD Pharmaceutical, Inc.: Employment, Equity Ownership. Lustgarten:ARIAD Pharmaceuticals Inc: Employment, Equity Ownership. Hawkins:Ariad Pharmaceuticals Inc.: Research Funding.

Characterization of the Genomic Landscape of BCR-ABL1 Kinase-Independent Mechanisms of Resistance to ABL1 Tyrosine Kinase Inhibitors in Chronic Myeloid Leukemia

Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 1119-1119 ◽  
Author(s):  
Christopher A. Eide ◽  
Daniel Bottomly ◽  
Samantha L. Savage ◽  
Libbey White ◽  
Beth Wilmot ◽  
...  
Keyword(s):  
Signaling Pathways ◽  
Board Of Directors ◽  
Research Funding ◽  
Kinase Inhibitors ◽  
Chronic Phase ◽  
Kinase Domain ◽  
Advisory Committees ◽  
Dana Farber Cancer Institute ◽  
Kinase Domain Mutation ◽  
Equity Ownership

Abstract Despite the well-established success of ABL1 tyrosine kinase inhibitors (TKIs) in the treatment of patients with chronic myeloid leukemia (CML), approximately 20% of patients treated with frontline imatinib develop resistance by 5 years on therapy. The majority (~60%) of such resistant cases are explained by acquired mutations within the BCR-ABL1 kinase domain that compromise inhibitor binding, and nearly all of these mutations are effectively targeted by one or more of the 2nd and 3rd generation ABL1 kinase inhibitors. In contrast, the remaining ~40% of imatinib-resistant cases harbor no explanatory BCR-ABL1 kinase domain mutation, presumably attributable to BCR-ABL1 kinase-independent mechanisms. We hypothesized that resistance in these patients results from acquired auxiliary molecular aberrations which persistently activate signaling pathways downstream despite inhibition of BCR-ABL1 kinase activity. To identify such mechanisms, we performed whole exome sequencing and RNA sequencing on a cohort of 135 CML patients comprising the following subgroups: newly diagnosed/TKI naïve (n=28), BCR-ABL1 kinase-dependent resistance (n=31), and BCR-ABL1 kinase-independent resistance (n=65), and TKI-induced remission (n=7). Resistant patients were required to have demonstrated clinical resistance to one or more ABL1 kinase inhibitors in the form of suboptimal response or loss of cytogenetic response; the subtype of resistance was defined based on the presence or not of an explanatory BCR-ABL1 kinase domain mutation at the time of resistance. The majority of samples collected were from patients with chronic phase CML (n=97), although smaller cohorts of accelerated phase CML, blast crisis CML, and Ph+ ALL were also profiled (n=20, 19, and 9, respectively). Among the 44,413 protein-altering and 902 splice site variants detected across the 120 WES samples, there were on average 908 missense, 146 truncation and 69 splice variants per sample. Genes with truncation and missense variants were compared between BCR-ABL1 kinase-independent and -dependent resistant chronic phase samples. A total of 44 genes were seen with a frequency difference of at least 10%, including PLEKHG5 and NKD2 (30% and 28% difference, respectively), which are involved in regulation of NF-kB and Wnt signaling. Consistent with previous reports, we also detected EZH2 and TET2 as exclusively mutated in the BCR-ABL1 kinase-independent resistance patients (6% and 3%, respectively). Further analyses stratifying variants among resistant patients according to specific ABL1 kinase inhibitor therapy failed and comparing, where available, serial samples from pre- and post-treatment for clonal expansion are underway. Additionally, sufficient material was available to perform ex vivo small-molecule inhibitor screening for 48 patient specimens, the resultant data of which was used to generate putative effective drug target profiles and integrated with exome sequencing variants to prioritize variants of functional relevance (HitWalker; Bottomly et al., Bioinformatics 2013). Among 23 patient samples exhibiting BCR-ABL1 kinase-independent resistance, the mutated genes most frequently ranked in the top 10 functional-prioritized variants were: ABL1 (which included non-kinase domain variants; 34.7%), MAP3K1, MUC4, FGF20 (each 17.4%), ARHGEF15, MEF2A, EPHA8, TYRO3, BMP2K, and IRS1 (each 13.0%). Notably, the top six candidates are members of the neutrophin (ABL1, MAP3K1, and IRS1), EPHA forward (EPHA8, ARHGEF15), and p38 MAPK signaling pathways (MAP3K1 and MEF2A). Taken together, these findings suggest that several of the same pathogenic molecular abnormalities seen in other myeloid malignancies are also present in CML patients with BCR-ABL1 kinase-independent resistance, including a subset which align to persistent re-activation of signaling pathways involved in CML disease pathogenesis and progression. As such, genetic and/or functional profiling of these patients in the clinic may translate to actionable candidates for combination therapy to maximize disease control and improve patient outcomes. Disclosures Agarwal: CTI BioPharma Corp: Research Funding. Radich:Novartis: Consultancy, Research Funding; BMS: Consultancy; Ariad: Consultancy. Deininger:Novartis: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding; Pfizer: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding; BMS: Consultancy, Research Funding; Incyte: Consultancy, Membership on an entity's Board of Directors or advisory committees; Gilead: Research Funding; CTI BioPharma Corp.: Membership on an entity's Board of Directors or advisory committees; Celgene: Research Funding; Bristol Myers Squibb: Consultancy, Research Funding; Ariad: Consultancy, Membership on an entity's Board of Directors or advisory committees. Druker:Pfizer: Patents & Royalties; Dana-Farber Cancer Institute: Patents & Royalties: Millipore royalties via Dana-Farber Cancer Institute; Curis: Patents & Royalties; Array: Patents & Royalties; CTI: Consultancy, Equity Ownership; Pfizer: Patents & Royalties; Curis: Patents & Royalties; Array: Patents & Royalties; Dana-Farber Cancer Institute: Patents & Royalties: Millipore royalties via Dana-Farber Cancer Institute; Oncotide Pharmaceuticals: Research Funding; Novartis: Research Funding; BMS: Research Funding; ARIAD: Patents & Royalties: inventor royalties paid by Oregon Health & Science University for licenses, Research Funding; Roche: Consultancy; Gilead Sciences: Consultancy, Other: travel, accommodations, expenses; D3 Oncology Solutions: Consultancy; AstraZeneca: Consultancy; Ambit BioSciences: Consultancy; Agios: Honoraria; MolecularMD: Consultancy, Equity Ownership, Patents & Royalties; Lorus: Consultancy, Equity Ownership; Cylene: Consultancy, Equity Ownership.

JAK1/2 and BCL2 Inhibitors Synergize to Counter-Act Bone Marrow Stromal Cell-Induced Protection of AML

Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 867-867
Author(s):  
Riikka Karjalalainen ◽  
Tea Pemovska ◽  
Muntasir Mamun Majumder ◽  
Bhagwan Yadav ◽  
Jing Tang ◽  
...  
Keyword(s):  
Bone Marrow ◽  
Cell Viability ◽  
Board Of Directors ◽  
Dose Response ◽  
Research Funding ◽  
Stromal Cell ◽  
Leukemic Cells ◽  
Jak Inhibitors ◽  
Advisory Committees ◽  
Equity Ownership

Abstract BACKGROUND AND OBJECTIVES: The bone marrow (BM) microenvironment supports the survival of leukemic cells and influences their response to therapeutic agents by promoting drug tolerance and resistance. Novel therapeutic strategies are therefore needed that can override the BM mediated protection of AML cells in patients undergoing drug treatment. To address this we used a high-throughput drug screening method to identify novel drug combinations to reverse stromal-induced cytoprotection against the BCL2 antagonist venetoclax in primary AML samples. METHODS: Sensitivity of mononuclear cells collected from 18 AML BM aspirates or peripheral blood samples to a range of BCL2 inhibitors and tyrosine kinase inhibitors (TKIs) was assessed either in mononuclear cell medium (MCM, Promocell) or in a 25% HS-5 stromal cell-conditioned medium plus 75% RPMI medium mix (CM) to mimic cytoprotective bone marrow conditions. Cell viability was measured after 72 h and dose response curves generated for each tested drug. Drug sensitivity scores were calculated based on the area under the dose response curve. For the drug combination studies single agents (venetoclax, WEHI-539, ruxolitinib) were added simultaneously at fixed concentrations to AML cells and incubated for 72 h either in the MCM or CM medium. Cell viability was measured using the CellTiter-Glo assay. The expression of BCL2 genes was measured by qPCR after incubating the AML patient cells in either MCM or CM for 48 h. RESULTS: Incubation of primary AML cells in the CM culture condition led to reduced sensitivity to BCL2 family inhibitors, suggesting that stromal-derived factors in the CM promote cytoprotection. This effect was particularly pronounced for the selective BCL2 inhibitor venetoclax, where the CM-induced loss of sensitivity coincided with decreased BCL2 expression and increased BCL2L1 expression. In contrast, JAK inhibitors showed improved efficacy in CM compared to MCM culture conditions. To determine if the protective effects of CM stromal-like conditions against venetoclax could be diminished, the drug was tested in combination with the JAK1/2 inhibitor ruxolitinib using AML cells cultured in MCM or CM. When tested on AML cells from 4 patients with the FLT3-ITD alteration, we found that ruxolitinib rescued the sensitivity of venetoclax in leukemic cells in the presence of CM and the combination of two drugs exhibited synergistic effects in this setting. The combinatorial activity, however, was not recapitulated in the MCM condition. Since CM was found to induce BCL2L1 expression, venetoclax was also tested in combination with a BCLXLspecific inhibitor WEHI-539. Analogously to the ruxolitinib-venetoclax combination, synergistic activity between venetoclax and WEHI-539 was observed towards leukemic cells in the presence of CM. CONCLUSIONS: By applying a functional, drug-based approach to understand microenvironment-induced mechanisms of drug resistance in AML, we found that the activity of the selective BCL2 inhibitor venetoclax towards AML cells is adversely affected in stromal-based conditions, while JAK inhibitors, in contrast, exhibit increased efficacy in these conditions. Our results suggest stroma-derived cytokines induce JAK-STAT signaling in AML cells, which results in increased BCL2L1 expression and drives resistance to venetoclax. However, blocking JAK1/2 with ruxolitinib restores the sensitivity of AML cells to venetoclax. We found that JAK1/2 inhibitors such as ruxolitinib can act synergistically with BCL2/BCLXL inhibitors, suggesting clinically useful combination treatments. Disclosures Gjertsen: BerGenBio AS: Equity Ownership, Membership on an entity's Board of Directors or advisory committees; Boehringer Ingelheim: Membership on an entity's Board of Directors or advisory committees; Kinn Therapeutics AS: Equity Ownership. Porkka:Pfizer: Honoraria, Research Funding; Bristol-Myers Squibb: Honoraria, Research Funding; Celgene: Honoraria, Research Funding; Novartis: Honoraria, Research Funding. Kallioniemi:Vysis-Abbot: Patents & Royalties; Medisapiens: Membership on an entity's Board of Directors or advisory committees; IMI-Project Predect: Research Funding; Roche: Research Funding; Pfizer: Research Funding. Wennerberg:Pfizer: Research Funding. Heckman:Celgene: Honoraria, Research Funding.

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