Study of Venetoclax in Combination With Azacytidine in AML Patients Selected Using Ex Vivo Drug Sensitivity Screening

Author(s):  
Keyword(s):  
2018 ◽  
Vol 25 (4) ◽  
pp. 471-480
Author(s):  
Kosmas Daskalakis ◽  
Olov Norlén ◽  
Andreas Karakatsanis ◽  
Per Hellman ◽  
Rolf Larsson ◽  
...  

Small intestinal neuroendocrine tumors (SI-NETs) are generally considered resistant to systemic treatment. To date, predictive markers for drug activity are lacking. Tumor samples from 27 patients with SI-NETs were analyzed ex vivo for sensitivity to a panel of cytotoxic drugs and targeted agents using a short-term total cell kill assay. Samples of renal cancer, colorectal cancer (CRC), ovarian cancer and chronic lymphocytic leukemia (CLL) were included for comparison. For the SI-NET subset, drug sensitivity was analyzed in relation to clinicopathological variables and pre-treatment biomarkers. For cytotoxic drugs, SI-NETs demonstrated similar or higher sensitivity to 5-FU, platinum, gemcitabine and doxorubicin compared with CRC. For several of the targeted kinase inhibitors, SI-NET was among the most sensitive solid tumor types. CLL and ovarian cancer were generally the most sensitive tumor types to both cytotoxic drugs and protein kinase inhibitors. SI-NET was more sensitive to the mTOR inhibitor sirolimus than the other solid tumor types tested. Individual SI-NET samples demonstrated great variability in ex vivo sensitivity for most drugs. Cross-resistance between different drugs also varied considerably, being higher among protein kinase inhibitors. Age, stage, grade, peritoneal carcinomatosis and extra-abdominal metastases as well as serum chromogranin A and urine 5-HIAA concentrations at diagnosis did not correlate to drug sensitivity ex vivo. SI-NETs exhibit intermediate sensitivity ex vivo to cytotoxic and targeted drugs. Clinicopathological factors and currently used biomarkers are not clearly associated to ex vivo sensitivity, challenging these criteria for treatment decisions in SI-NET. The great variability in drug sensitivity calls for individualized selection of therapy.


Author(s):  
Cristina E. Tognon ◽  
Rosalie C. Sears ◽  
Gordon B. Mills ◽  
Joe W. Gray ◽  
Jeffrey W. Tyner

The use of ex vivo drug sensitivity testing to predict drug activity in individual patients has been actively explored for almost 50 years without delivering a generally useful predictive capability. However, extended failure should not be an indicator of futility. This is especially true in cancer research, where ultimate success is often preceded by less successful attempts. For example, both immune- and genetic-based targeted therapies for cancer underwent numerous failed attempts before biological understanding, improved targets, and optimized drug development matured to facilitate an arsenal of transformational drugs. Similarly, directly assessing drug sensitivity of primary tumor biopsies—and the use of this information to help direct therapeutic approaches—has a long history with a definitive learning curve. In this review, we survey the history of ex vivo testing and the current state of the art for this field. We present an update on methodologies and approaches, describe the use of these technologies to test cutting-edge drug classes, and describe an increasingly nuanced understanding of tumor types and models for which this strategy is most likely to succeed. We consider the relative strengths and weaknesses of predicting drug activity across the broad biological context of cancer patients and tumor types. This includes an analysis of the potential for ex vivo drug sensitivity testing to accurately predict drug activity within each of the biological hallmarks of cancer pathogenesis. Expected final online publication date for the Annual Review of Cancer Biology, Volume 5 is March 4, 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.


Blood ◽  
2018 ◽  
Vol 132 (Supplement 1) ◽  
pp. 4356-4356 ◽  
Author(s):  
Alexey Aleshin ◽  
Marianne A Santaguida ◽  
Michael A Spinner ◽  
Jeffrey N Sanders ◽  
A Scott Patterson ◽  
...  

Abstract Introduction: Myelodysplastic syndromes (MDS), chronic myelomonocytic leukemia (CMML) and acute myeloid leukemia (AML) are clonal myeloid neoplasms for which limited conventional treatment options exist in the relapsed / refractory setting, especially for older patients. Methods: We provide proof of concept data by drug sensitivity profiling of 64 samples from 52 adult patients with both newly diagnosed and treatment refractory myeloid neoplasms (MDS = 38, CMML = 4, AML = 10). Fresh mononuclear cells from bone marrow aspirates and/or peripheral blood specimens were red blood cell lysed upon arrival and re-suspended in serum free media with cytokines. The samples were then plated in 384 well microtiter plates and were screened against a collection of investigational and FDA approved compounds (up to 85) in triplicate using a Labcyte Echo acoustic liquid handler. These specimens were treated for 72 hours and analyzed for drug sensitivity on an Intellicyt iQue Screener PLUS flow cytometer for both cytotoxicity and differentiation. Results: Principal component analysis was performed to explore differential ex vivo sensitivity and resistance patterns between the MDS and AML samples. Individual MDS samples clustered according to their ex vivo responses, with distinct subgroups enriched for sensitivity to hypomethylating agents (HMAs), HDAC inhibitors, differentiation agents, and PARP inhibitors. Strong clustering of drug classes was also observed with distinct drug classes showing high correlation within samples. Clinical parameters contributed but did not explain all of the variability of ex vivo sensitivity patterns, including prior HMA therapy, cytogenetics, prognostic risk category and mutational profile. In patients resistant to or relapsed from HMAs where next line of treatment matched profiled compounds (n = 19), ex vivo drug sensitivity data demonstrated positive (PPV) and negative predictive values (NPV) of 85% and 83%, respectively, for clinical response prediction (Fisher's exact test p-value = 0.0095). In patients with serial samples, ex vivo sensitivity data corresponded to emergence of clinical resistance. Conclusions: This novel platform, applied to predict ex vivo therapeutic responses of patient samples to various classes of drugs, recapitulates known clinical and molecular predictors of therapeutic efficacy and provides possible new biologically focused therapeutic options. The accuracy and reproducibility of this method coupled with short turnaround time demonstrate the potential of such an approach as a decision support system for therapeutic selection in the management of various myeloid neoplasms. A prospective study is ongoing to assess the feasibility of this technique for treatment decision support purposes in HMA-refractory MDS patients. Disclosures Aleshin: Mission Bio, Inc.: Consultancy; Natera, Inc.: Employment. Santaguida:Notable Labs: Employment. Patterson:Notable Labs: Employment. Gekas:Notable Labs: Employment. Schaffert:Notable Labs: Consultancy.


Blood ◽  
2020 ◽  
Vol 136 (Supplement 1) ◽  
pp. 37-38
Author(s):  
Olivia Perez De Acha ◽  
Beau M Idler ◽  
Zachary J Walker ◽  
Peter A Forsberg ◽  
Tomer M Mark ◽  
...  

Background: Daratumumab-refractory multiple myeloma (MM) patients have limited treatment options and a dire prognosis. Daratumumab (Dara) targets the overexpressed myeloma antigen CD38, and its mechanism of resistance has been partially associated with downregulation of CD38 expression (Nijhof et al. Blood, 2016). Dara is a key agent in the relapsed setting and is being integrated into upfront treatment. In addition, isatuximab (Isa) has become the second FDA-approved anti-CD38 monoclonal antibody (mAb). Thus, when and how patients can be retreated with this important drug-class has become a critical question. We developed a platform for measuring drug efficacy ex vivo, including mAbs, termed Myeloma Drug Sensitivity Testing (My-DST) (Walker et al. Blood Advances, 2020). Here, we addressed whether My-DST could determine if retreatment with the anti-CD38 mAbs Dara and Isa can be effective in patients that had previously developed Dara-resistance. Methods: Bone marrow aspirates were obtained from the hematologic tissue bank (HTB) from patients at the University of Colorado Blood Cancer Program after informed consent and IRB approval. Mononuclear cells (MNCs) were isolated by Ficoll density gradient centrifugation, cells incubated for 48 h with 20 nM Dara, Isa and untreated controls in triplicate wells. Flow cytometry was performed on a BD FACSCelesta. To identify the viable MM population, samples were stained with fluorophore-conjugated mAbs to CD38, CD138, CD45, CD19, CD56 and CD46. Stained samples were washed and resuspended in Live/Dead dye Near-IR. Results were analyzed through FlowJo and Graphpad Prism software. Results: My-DST for Dara (20 nM) cytotoxicity has been performed in 67 patients, 52 of which were Dara-naïve and 15 of which were clinically Dara-refractory. Of Dara-naïve patients, 38/52 (73%) showed >20% reduction in viable MM cells whereas only 3/15 (20%) of the Dara-refractory patients showed >20% decrease (Fig 1A). Provocatively, the patients that showed potential "re-sensitization" had been off Dara for >12 months, and there was a significant correlation between response to Dara and months off treatment (r= -0.5096, p= 0.0457, Fig 1B). Furthermore, we evaluated two timepoints in one of the responders (HTB1749), and the later sample (HTB1749.3) showed a deeper response, further supporting the correlation. Surprisingly, in Dara-refractory patients the median CD38 expression was not significantly different between the three ex vivo responders and those who did not respond (p = 0.439, Fig 1C). Isa was tested in seven of the Dara-refractory patient samples, showing >20% decrease in viable MM cells in five, of which three did not respond ex vivo to Dara (Fig 1D). Interestingly, the Isa responders were only off Dara treatment for an average of 7.5 months. We further investigated HTB1059.3 and HTB1749.2, which responded to Dara, and found that these patients had multiple distinct MM cell subpopulations with different levels of CD38 expression, with the subpopulation with higher CD38 MFI accounting for the decreased viability (Fig 1E-F). When we compared HTB1059.3 with a prior sample available, these differential populations were not present before Dara treatment (data not shown), indicating these subpopulations evolved after treatment. Likewise, the same phenomenon of subpopulations with differential CD38 expression was observed in the Dara-refractory patients who responded to Isa (Fig 1G-H). Conclusion: These data support the possibility of retreatment with anti-CD38 mAbs in patients who once became refractory to Dara. Although our findings need to be confirmed with additional samples, they suggest that Isa may have efficacy earlier in this setting, supporting an approach to switch agents when retreating with this drug class. Anti-CD38 mAb sensitivity in the Dara-refractory population appears to be heavily influenced by the different CD38 expression levels on the heterogeneous MM cell subpopulations that emerge when a patient is off Dara for a period of time. Furthermore, My-DST with anti-CD38 mAbs may be applied to help guide the treatment approach in this population. Still, the presence of CD38-low subpopulations in these patients may represent resistant cells that shorten the remission times on retreatment. Thus, the combination drug partner choice will likely be critical to successfully optimizing depth and duration of response in Dara-refractory patients. Figure 1 Disclosures Forsberg: Genentech, Inc., Sanofi, Karyopharm, Abbvie: Research Funding; Celgene: Speakers Bureau. Mark:Bristol-Myers Squibb: Research Funding; Janssen: Research Funding; Celgene: Consultancy; Amgen: Consultancy; Kayopharm: Consultancy; Janssen: Consultancy; Sanofi: Consultancy; Takeda: Consultancy. Sherbenou:Oncopeptides Inc.: Research Funding.


2021 ◽  
Vol 39 (15_suppl) ◽  
pp. e19013-e19013
Author(s):  
Marianne T. Santaguida ◽  
Ryosuke Kita ◽  
Steven A. Schaffert ◽  
Erica K. Anderson ◽  
Kamran A Ali ◽  
...  

e19013 Background: Understanding the heterogeneity of AML is necessary for developing targeted drugs and diagnostics. A key measure of heterogeneity is the variance in response to treatments. Previously, we developed an ex vivo flow cytometry drug sensitivity assay (DSA) that predicted response to treatments in myelodysplastic syndrome. Unlike bulk cell viability measures of other drug sensitivity assays, our flow cytometry assay provides single cell resolution. The assay measures a drug’s effect on the viability or functional state of specific cell types. Here we present the development of this technology for AML, with additional measurements of DNA-Seq and RNA-Seq. Using the data from this assay, we aim to characterize the heterogeneity in AML drug sensitivity and the molecular mechanisms that drive it. Methods: As an initial feasibility analysis, we assayed 1 bone marrow and 3 peripheral blood AML patient samples. For the DSA, the samples were cultured with six AML standard of care (SOC) compounds across seven doses, in addition to two combinations. The cells were stained to detect multiple cell types including tumor blasts, and drug response was measured by flow cytometry. For the multi-omics, the cells were magnetically sorted to enrich for blasts and then assayed using a targeted 400 gene DNA-Seq panel and whole bulk transcriptome RNA-Seq. For comparison with BeatAML, Pearson correlations between gene expression and venetoclax sensitivity were investigated. Results: In our drug sensitivity assay, we measured dose response curves for the six SOC compounds, for each different cell type across each sample. The dose responses had cell type specific effects, including differences in drug response between CD11b+ blasts, CD11b- blasts, and other non-blast populations. Integrating with the DNA-Seq and RNA-Seq data, known associations between ex vivo drug response and gene expression were identified with additional cell type specificity. For example, BCL2A1 expression was negatively correlated with venetoclax sensitivity in CD11b- blasts but not in CD11b+ blasts. To further corroborate, among the top 1000 genes associated with venetoclax sensitivity in BeatAML, 93.7% had concordant directionality in effect. Conclusions: Here we describe the development of an integrated ex vivo drug sensitivity assay and multi-omics dataset. The data demonstrated that ex vivo responses to compounds differ between cell types, highlighting the importance of measuring drug response in specific cell types. In addition, we demonstrated that integrating these data will provide unique insights on molecular mechanisms that affect cell type specific drug response. As we continue to expand the number of patient samples evaluated with our multi-dimensional platform, this dataset will provide insights for novel drug target discovery, biomarker development, and, in the future, informing treatment decisions.


2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Sanjay de Mel ◽  
Masturah B. M. Rashid ◽  
Xi Yun Zhang ◽  
Jasmine Goh ◽  
Chun Tsu Lee ◽  
...  

2019 ◽  
Author(s):  
Sergey G. Kuznetsov ◽  
Alexander Ianevski ◽  
Evgeny Kulessky ◽  
Karoliina Laamanen ◽  
Elina Lehtinen ◽  
...  

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