Phenotype-based drug screening reveals association between venetoclax response and differentiation stage in acute myeloid leukemia

Kuusanmäki, Heikki; Leppä, Aino-Maija; Pölönen, Petri; Kontro, Mika; Dufva, Olli; Deb, Debashish; Yadav, Bhagwan; Brück, Oscar; Kumar, Ashwini; Everaus, Hele; Gjertsen, Bjørn Tore; Heinäniemi, Merja; Porkka, Kimmo; Mustjoki, Satu; Heckman, Caroline A.

doi:10.3324/haematol.2018.214882

Cited by 122 publications

(133 citation statements)

References 44 publications

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“…Likewise, we were not able to demonstrate a statistically significant difference in BCL-2 protein expression level between CD34 + and CD34 − AML patients, whereas others have shown that BCL-2 is maximally expressed in the CD34 + leukemic cell compartment, followed by a downregulation upon the loss of CD34 during differentiation [ 25 , 31 , 32 ]. In line with two recent studies demonstrating lower BCL-2 gene expression levels in AMLs with a monocytic component [ 33 , 34 ], we observed lower BCL-2 protein levels in monocytic AML. This might, at least in part, explain why AMLs with a monocytic phenotype tend to be more resistant to venetoclax-based therapy.…”

Section: Discussionsupporting

confidence: 92%

Absence of BCL-2 Expression Identifies a Subgroup of AML with Distinct Phenotypic, Molecular, and Clinical Characteristics

haes

Dendooven

Mercier

et al. 2020

JCM

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Acute myeloid leukemia (AML) is a hematologic malignancy characterized by the rapid and uncontrolled clonal growth of myeloid lineage cells in the bone marrow. The advent of oral, selective inhibitors of the B-cell leukemia/lymphoma-2 (BCL-2) apoptosis pathway, such as venetoclax, will likely induce a paradigm shift in the treatment of AML. However, the high cost of this treatment and the risk of additive toxicity when used in combination with standard chemotherapy represent limitations to its use and underscore the need to identify which patients are most—and least—likely to benefit from incorporation of venetoclax into the treatment regimen. Bone marrow specimens from 93 newly diagnosed AML patients were collected in this study and evaluated for BCL-2 protein expression by immunohistochemistry. Using this low-cost, easily, and readily applicable analysis method, we found that 1 in 5 AML patients can be considered as BCL-2−. In addition to a lower bone marrow blast percentage, this group exhibited a favorable molecular profile characterized by lower WT1 expression and underrepresentation of FLT3 mutations. As compared to their BCL-2+ counterparts, the absence of BCL-2 expression was associated with a favorable response to standard chemotherapy and overall survival, thus potentially precluding the necessity for venetoclax add-on.

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Section: Discussionsupporting

confidence: 92%

Absence of BCL-2 Expression Identifies a Subgroup of AML with Distinct Phenotypic, Molecular, and Clinical Characteristics

haes

Dendooven

Mercier

et al. 2020

JCM

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“…Table 2). The potency of navitoclax is in line with our earlier observation of higher activity of Bcl-2 inhibitors in M1 subtype AML 42 . In general, the patient sample showed a high selective sensitivity (sDSS range 13-21) to a number of targeted compounds, including kinase inhibitors, HSP inhibitors and apoptotic modulators (Suppl .…”

Section: Aml3 Patient (Diagnosis Stage)supporting

confidence: 89%

“…Next-generation functional precision medicine approaches that combine bulk molecular and genomic characterization of individual patient samples at various disease stages with the whole-well ex-vivo phenotypic profiling of the patient samples using large compound libraries has demonstrated to provide a relatively fast and practical platform for translational discoveries in hematological malignancies both for monotherapies and combination discoveries [51][52][53][54] . High-throughput flow cytometry-based profiling approaches have been stablished to further evaluate the ex vivo sensitivity of various cell populations in primary AML samples 42 , where especially refractory patient samples often have lower blast cell percentages, making the whole-well viability assays less reliable for drug response profiling. However, flow cytometry profiling of a larger number of drug combinations in multiple doses is currently not feasible in scarce primary patient cells; instead, translational strategies rely on testing only selected drugs or combinations in single concentrations 55 .…”

Section: Discussionmentioning

confidence: 99%

“…We performed HTFC assays to assess the effects of drugs on multiple cell populations in primary AML patient samples, as described previosly 42 . Briefly, the compounds were dissolved in 100% DMSO or an aqueous solution and dispensed on tissue culture grade Corning V-bottom 96-well plates using an Echo 550 Liquid Handler (Labcyte) in 4 concentrations of 10-fold dilution series around the IC50 (Suppl .…”

Section: Investigation Of the Combination Using High-throughput Flow mentioning

confidence: 99%

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Patient-tailored design of AML cell subpopulation-selective drug combinations

Ianevski

Lahtela

Javarappa

et al. 2020

Preprint

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The extensive primary and secondary drug resistance in acute myeloid leukemia (AML) requires rational approaches to design personalized combinatorial treatments that exploit patient-specific therapeutic vulnerabilities to optimally target disease-driving AML cell subpopulations. However, the large number of AML-relevant drug combinations makes the testing impossible in scarce primary patient cells. This combinatorial problem is further exacerbated by the translational challenge of how to design such personalized and selective drug combinations that do not only show synergistic effect in overall AML cell killing but also result in minimal toxic side effects on non-malignant cells. To solve these challenges, we implemented a systematic computational-experimental approach for identifying potential drug combinations that have a desired synergy-efficacy-toxicity balance. Our mechanism-agnostic approach combines single-cell RNA-sequencing (scRNA-seq) with ex vivo single-agent viability testing in primary patient cells. The data integration and predictive modelling are carried out at a single-cell resolution by means of a machine learning model that makes use of compound-target interaction networks to narrow down the massive search space of potentially effective drug combinations. When applied to two diagnostic and two refractory AML patient cases, each having a different genetic background, our integrated approach predicted a number of patient-specific combinations that were shown to result not only in synergistic cancer cell inhibition but were also capable of targeting specific AML cell subpopulations that emerge in differing stages of disease pathogenesis or treatment regimens. Overall, 53% of the 59 predicted combinations were experimentally confirmed to show synergy, and 83% were non-antagonistic, as validated with viability assays, which is a significant improvement over the success rate of randomly guessing a synergistic drug combination (5%). Importantly, 67% of the predicted combinations showed low toxicity to non-malignant cells, as validated with flow-based population assays, suggesting their selective killing of AML cell populations. Our data-driven approach provides an unbiased means for systematic prioritization of patient-specific drug combinations that selectively inhibit AML cells and avoid co-inhibition of non-malignant cells, thereby increasing their likelihood for clinical translation. The approach uses only a limited number of patient primary cells, and it is widely applicable to hematological cancers that are accessible for scRNA-seq profiling and ex vivo compound testing.

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“…This data confirmed findings previously demonstrated in T-ALL (20,35,36) and other cancers. (37)(38)(39) Ruxolitinib treatment alone has been considered a breakthrough therapy for myeloproliferative neoplasms but long-term studies have shown that this treatment is not curative and does not lead to molecular or pathological remission. This may be caused by the This xenograft model is clinically relevant given that CNS relapse is common for T-ALL, and is a strong driver for a poor prognosis.…”

Section: Discussionmentioning

confidence: 99%

CXCR4 allows T cell acute lymphoblastic leukemia to escape from JAK1/2 and BCL2 inhibition through CNS infiltration

Walker

Kabakov

Zhu

et al. 2019

Preprint

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Relapsed/refractory T cell acute lymphoblastic leukemia (T-ALL) is difficult to salvage especially in heavily pretreated patients, thus novel targeted agents are sorely needed.Hyperactivated JAK/STAT and BCL2 overexpression promote increased T-ALL proliferation and survival, and targeting these pathways with ruxolitinib and venetoclax may provide an alternative approach to achieve clinical remissions. Ruxolitinib and venetoclax show a dosedependent effect individually, but combination treatment synergistically reduces survival and proliferation of Jurkat and Loucy cells in vitro. Using a xenograft CXCR4+ Jurkat model, the combination treatment fails to improve survival, with death from hind limb paralysis. Despite ontarget inhibition by the drugs, histopathology demonstrates increased leukemic infiltration into the central nervous system (CNS), which expresses CXCL12, as compared to liver or bone marrow. Liquid chromatography-tandem mass spectroscopy shows that neither ruxolitinib nor venetoclax can effectively cross the blood-brain barrier, limiting efficacy against CNS T-ALL.Deletion of CXCR4 on Jurkat cells by CRISPR/Cas9 results in prolonged survival and a reduction in overall and neurologic clinical scores. While combination therapy with ruxolitinib and venetoclax shows promise for treating T-ALL, additional inhibition of the CXCR4-CXCL12 axis will be needed to eliminate both systemic and CNS T-ALL burden and maximize the possibility of complete remission.

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Phenotype-based drug screening reveals association between venetoclax response and differentiation stage in acute myeloid leukemia

Cited by 122 publications

References 44 publications

Absence of BCL-2 Expression Identifies a Subgroup of AML with Distinct Phenotypic, Molecular, and Clinical Characteristics

Absence of BCL-2 Expression Identifies a Subgroup of AML with Distinct Phenotypic, Molecular, and Clinical Characteristics

Patient-tailored design of AML cell subpopulation-selective drug combinations

CXCR4 allows T cell acute lymphoblastic leukemia to escape from JAK1/2 and BCL2 inhibition through CNS infiltration

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