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Adnan Awad S, Dufva O, Klievink J, Karjalainen E, Ianevski A, Pietarinen P, Kim D, Potdar S, Wolf M, Lotfi K, Aittokallio T, Wennerberg K, Porkka K, Mustjoki S. Integrated drug profiling and CRISPR screening identify BCR::ABL1-independent vulnerabilities in chronic myeloid leukemia. Cell Rep Med 2024; 5:101521. [PMID: 38653245 PMCID: PMC11148568 DOI: 10.1016/j.xcrm.2024.101521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 01/10/2024] [Accepted: 03/27/2024] [Indexed: 04/25/2024]
Abstract
BCR::ABL1-independent pathways contribute to primary resistance to tyrosine kinase inhibitor (TKI) treatment in chronic myeloid leukemia (CML) and play a role in leukemic stem cell persistence. Here, we perform ex vivo drug screening of CML CD34+ leukemic stem/progenitor cells using 100 single drugs and TKI-drug combinations and identify sensitivities to Wee1, MDM2, and BCL2 inhibitors. These agents effectively inhibit primitive CD34+CD38- CML cells and demonstrate potent synergies when combined with TKIs. Flow-cytometry-based drug screening identifies mepacrine to induce differentiation of CD34+CD38- cells. We employ genome-wide CRISPR-Cas9 screening for six drugs, and mediator complex, apoptosis, and erythroid-lineage-related genes are identified as key resistance hits for TKIs, whereas the Wee1 inhibitor AZD1775 and mepacrine exhibit distinct resistance profiles. KCTD5, a consistent TKI-resistance-conferring gene, is found to mediate TKI-induced BCR::ABL1 ubiquitination. In summary, we delineate potential mechanisms for primary TKI resistance and non-BCR::ABL1-targeting drugs, offering insights for optimizing CML treatment.
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MESH Headings
- Humans
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/metabolism
- Fusion Proteins, bcr-abl/genetics
- Fusion Proteins, bcr-abl/metabolism
- Fusion Proteins, bcr-abl/antagonists & inhibitors
- Protein Kinase Inhibitors/pharmacology
- CRISPR-Cas Systems/genetics
- Drug Resistance, Neoplasm/genetics
- Drug Resistance, Neoplasm/drug effects
- Proto-Oncogene Proteins c-abl/metabolism
- Proto-Oncogene Proteins c-abl/genetics
- Proto-Oncogene Proteins c-abl/antagonists & inhibitors
- Cell Line, Tumor
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Affiliation(s)
- Shady Adnan Awad
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; Foundation for the Finnish Cancer Institute, 00290 Helsinki, Finland; Clinical Pathology Department, National Cancer Institute, Cairo University, 11796 Cairo, Egypt.
| | - Olli Dufva
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00014 Helsinki, Finland
| | - Jay Klievink
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland
| | - Ella Karjalainen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute for Life Science, University of Helsinki, 00014 Helsinki, Finland
| | - Aleksandr Ianevski
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute for Life Science, University of Helsinki, 00014 Helsinki, Finland
| | - Paavo Pietarinen
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland
| | - Daehong Kim
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland
| | - Swapnil Potdar
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute for Life Science, University of Helsinki, 00014 Helsinki, Finland
| | - Maija Wolf
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute for Life Science, University of Helsinki, 00014 Helsinki, Finland
| | - Kourosh Lotfi
- Department of Medical and Health Sciences, Faculty of Medicine and Health, Linköping University, 58183 Linköping, Sweden
| | - Tero Aittokallio
- Foundation for the Finnish Cancer Institute, 00290 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00014 Helsinki, Finland; Institute for Molecular Medicine Finland (FIMM), Helsinki Institute for Life Science, University of Helsinki, 00014 Helsinki, Finland; Institute for Cancer Research, Oslo University Hospital, 0424 Oslo, Norway; Oslo Centre for Biostatistics and Epidemiology, University of Oslo, 0317 Oslo, Norway
| | - Krister Wennerberg
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute for Life Science, University of Helsinki, 00014 Helsinki, Finland; Biotech Research & Innovation Centre and Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, 2200 Copenhagen, Denmark
| | - Kimmo Porkka
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00014 Helsinki, Finland
| | - Satu Mustjoki
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00014 Helsinki, Finland.
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2
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Ali KA, Shah RD, Dhar A, Myers NM, Nguyen C, Paul A, Mancuso JE, Scott Patterson A, Brody JP, Heiser D. Ex vivo discovery of synergistic drug combinations for hematologic malignancies. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2024; 29:100129. [PMID: 38101570 DOI: 10.1016/j.slasd.2023.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/13/2023] [Accepted: 12/09/2023] [Indexed: 12/17/2023]
Abstract
Combination therapies have improved outcomes for patients with acute myeloid leukemia (AML). However, these patients still have poor overall survival. Although many combination therapies are identified with high-throughput screening (HTS), these approaches are constrained to disease models that can be grown in large volumes (e.g., immortalized cell lines), which have limited translational utility. To identify more effective and personalized treatments, we need better strategies for screening and exploring potential combination therapies. Our objective was to develop an HTS platform for identifying effective combination therapies with highly translatable ex vivo disease models that use size-limited, primary samples from patients with leukemia (AML and myelodysplastic syndrome). We developed a system, ComboFlow, that comprises three main components: MiniFlow, ComboPooler, and AutoGater. MiniFlow conducts ex vivo drug screening with a miniaturized flow-cytometry assay that uses minimal amounts of patient sample to maximize throughput. ComboPooler incorporates computational methods to design efficient screens of pooled drug combinations. AutoGater is an automated gating classifier for flow cytometry that uses machine learning to rapidly analyze the large datasets generated by the assay. We used ComboFlow to efficiently screen more than 3000 drug combinations across 20 patient samples using only 6 million cells per patient sample. In this screen, ComboFlow identified the known synergistic combination of bortezomib and panobinostat. ComboFlow also identified a novel drug combination, dactinomycin and fludarabine, that synergistically killed leukemic cells in 35 % of AML samples. This combination also had limited effects in normal, hematopoietic progenitors. In conclusion, ComboFlow enables exploration of massive landscapes of drug combinations that were previously inaccessible in ex vivo models. We envision that ComboFlow can be used to discover more effective and personalized combination therapies for cancers amenable to ex vivo models.
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Affiliation(s)
- Kamran A Ali
- Notable Labs, 320 Hatch Dr, Foster City, CA, 94404, USA; Department of Biomedical Engineering, University of California, Irvine, 3120 Natural Sciences II, Irvine, CA, 92697, USA.
| | - Reecha D Shah
- Notable Labs, 320 Hatch Dr, Foster City, CA, 94404, USA
| | - Anukriti Dhar
- Notable Labs, 320 Hatch Dr, Foster City, CA, 94404, USA
| | - Nina M Myers
- Notable Labs, 320 Hatch Dr, Foster City, CA, 94404, USA
| | | | - Arisa Paul
- Notable Labs, 320 Hatch Dr, Foster City, CA, 94404, USA
| | | | | | - James P Brody
- Department of Biomedical Engineering, University of California, Irvine, 3120 Natural Sciences II, Irvine, CA, 92697, USA
| | - Diane Heiser
- Notable Labs, 320 Hatch Dr, Foster City, CA, 94404, USA
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3
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Andersen AN, Brodersen AM, Ayuda-Durán P, Piechaczyk L, Tadele DS, Baken L, Fredriksen J, Stoksflod M, Lenartova A, Fløisand Y, Skånland SS, Enserink JM. Clinical forecasting of acute myeloid leukemia using ex vivo drug-sensitivity profiling. CELL REPORTS METHODS 2023; 3:100654. [PMID: 38065095 PMCID: PMC10753296 DOI: 10.1016/j.crmeth.2023.100654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 09/16/2023] [Accepted: 11/09/2023] [Indexed: 12/21/2023]
Abstract
Current treatment selection for acute myeloid leukemia (AML) patients depends on risk stratification based on cytogenetic and genomic markers. However, the forecasting accuracy of treatment response remains modest, with most patients receiving intensive chemotherapy. Recently, ex vivo drug screening has gained traction in personalized treatment selection and as a tool for mapping patient groups based on relevant cancer dependencies. Here, we systematically evaluated the use of drug sensitivity profiling for predicting patient survival and clinical response to chemotherapy in a cohort of AML patients. We compared computational methodologies for scoring drug efficacy and characterized tools to counter noise and batch-related confounders pervasive in high-throughput drug testing. We show that ex vivo drug sensitivity profiling is a robust and versatile approach to patient prognostics that comprehensively maps functional signatures of treatment response and disease progression. In conclusion, ex vivo drug profiling can assess risk for individual AML patients and may guide clinical decision-making.
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Affiliation(s)
- Aram N Andersen
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Montebello, 0379 Oslo, Norway; Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Blindern, 0318 Oslo, Norway; Section for Biochemistry and Molecular Biology, Faculty of Mathematics and Natural Sciences, University of Oslo, Blindernveien 31, 0371 Oslo, Norway.
| | - Andrea M Brodersen
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Montebello, 0379 Oslo, Norway; Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Blindern, 0318 Oslo, Norway; Section for Biochemistry and Molecular Biology, Faculty of Mathematics and Natural Sciences, University of Oslo, Blindernveien 31, 0371 Oslo, Norway
| | - Pilar Ayuda-Durán
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Montebello, 0379 Oslo, Norway; Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Blindern, 0318 Oslo, Norway
| | - Laure Piechaczyk
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Montebello, 0379 Oslo, Norway; Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Blindern, 0318 Oslo, Norway
| | - Dagim Shiferaw Tadele
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Montebello, 0379 Oslo, Norway; Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Blindern, 0318 Oslo, Norway
| | - Lizet Baken
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Montebello, 0379 Oslo, Norway; Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Blindern, 0318 Oslo, Norway
| | - Julia Fredriksen
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Montebello, 0379 Oslo, Norway; Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Blindern, 0318 Oslo, Norway; Department of Haematology, Oslo University Hospital, 0372 Oslo, Norway
| | - Mia Stoksflod
- Department of Haematology, Oslo University Hospital, 0372 Oslo, Norway
| | - Andrea Lenartova
- Department of Haematology, Oslo University Hospital, 0372 Oslo, Norway
| | - Yngvar Fløisand
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Blindern, 0318 Oslo, Norway
| | - Sigrid S Skånland
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Montebello, 0379 Oslo, Norway; K.G. Jebsen Centre for B Cell Malignancies, Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway
| | - Jorrit M Enserink
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Montebello, 0379 Oslo, Norway; Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Blindern, 0318 Oslo, Norway; Section for Biochemistry and Molecular Biology, Faculty of Mathematics and Natural Sciences, University of Oslo, Blindernveien 31, 0371 Oslo, Norway.
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4
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Stieglitz E, Gu CJ, Richardson M, Kita R, Santaguida MT, Ali KA, Strachan DC, Dhar A, Yam G, Anderson W, Anderson E, Hübner J, Tasian SK, Loh ML, Lacher MD. Tretinoin Enhances the Effects of Chemotherapy in Juvenile Myelomonocytic Leukemia Using an Ex Vivo Drug Sensitivity Assay. JCO Precis Oncol 2023; 7:e2300302. [PMID: 37944074 PMCID: PMC10645413 DOI: 10.1200/po.23.00302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 08/09/2023] [Accepted: 08/24/2023] [Indexed: 11/12/2023] Open
Abstract
PURPOSE Juvenile myelomonocytic leukemia (JMML) is an aggressive pediatric malignancy with myelodysplastic and myeloproliferative features. Curative treatment is restricted to hematopoietic stem-cell transplantation. Fludarabine combined with cytarabine (FLA) and 5-azacitidine (AZA) monotherapy are commonly used pre-transplant therapies. Here, we present a drug screening strategy using a flow cytometry-based precision medicine platform to identify potential additional therapeutic vulnerabilities. METHODS We screened 120 dual- and 10 triple-drug combinations (DCs) on peripheral blood (n = 21) or bone marrow (n = 6) samples from 27 children with JMML to identify DCs more effectively reducing leukemic cells than the DCs' components on their own. If fewer leukemic cells survived a DC ex vivo treatment compared with that DC's most effective component alone, the drug effect was referred to as cooperative. The difference between the two resistant fractions is the effect size. RESULTS We identified 26 dual- and one triple-DC more effective than their components. The differentiation agent tretinoin (TRET; all-trans retinoic acid) reduced the resistant fraction of FLA in 19/21 (90%) samples (decrease from 15% [2%-61%] to 11% [2%-50%] with a mean effect size of 3.8% [0.5%-11%]), and of AZA in 19/25 (76%) samples (decrease from 69% [34%-100+%] to 47% [17%-83%] with a mean effect size of 16% [0.3%-40%]). Among the resistant fractions, the mean proportion of CD38+ cells increased from 7% (0.03%-25%; FLA) to 17% (0.3%-38%; FLA + TRET) or from 10% (0.2%-31%; AZA) to 51% (0.8%-88%; AZA + TRET). CONCLUSION TRET enhanced the effects of FLA and AZA in ex vivo assays with primary JMML samples.
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Affiliation(s)
- Elliot Stieglitz
- University of California San Francisco, Benioff Children's Hospital, San Francisco, CA
| | | | | | | | | | | | | | | | | | | | | | - Juwita Hübner
- University of California San Francisco, Benioff Children's Hospital, San Francisco, CA
| | - Sarah K. Tasian
- Children's Hospital of Philadelphia, Division of Oncology and Center for Childhood Cancer Research and University of Pennsylvania School of Medicine, Philadelphia, PA
| | - Mignon L. Loh
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute and Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, WA
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5
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Rovsing AB, Thomsen EA, Nielsen I, Skov TW, Luo Y, Dybkaer K, Mikkelsen JG. Resistance to vincristine in DLBCL by disruption of p53-induced cell cycle arrest and apoptosis mediated by KIF18B and USP28. Br J Haematol 2023; 202:825-839. [PMID: 37190875 DOI: 10.1111/bjh.18872] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/21/2023] [Accepted: 05/04/2023] [Indexed: 05/17/2023]
Abstract
The frontline therapy R-CHOP for patients with diffuse large B-cell lymphoma (DLBCL) has remained unchanged for two decades despite numerous Phase III clinical trials investigating new alternatives. Multiple large studies have uncovered genetic subtypes of DLBCL enabling a targeted approach. To further pave the way for precision oncology, we perform genome-wide CRISPR screening to uncover the cellular response to one of the components of R-CHOP, vincristine, in the DLBCL cell line SU-DHL-5. We discover important pathways and subnetworks using gene-set enrichment analysis and protein-protein interaction networks and identify genes related to mitotic spindle organization that are essential during vincristine treatment. The inhibition of KIF18A, a mediator of chromosome alignment, using the small molecule inhibitor BTB-1 causes complete cell death in a synergistic manner when administered together with vincristine. We also identify the genes KIF18B and USP28 of which CRISPR/Cas9-directed knockout induces vincristine resistance across two DLBCL cell lines. Mechanistic studies show that lack of KIF18B or USP28 counteracts a vincristine-induced p53 response suggesting that resistance to vincristine has origin in the mitotic surveillance pathway (USP28-53BP1-p53). Collectively, our CRISPR screening data uncover potential drug targets and mechanisms behind vincristine resistance, which may support the development of future drug regimens.
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Affiliation(s)
| | | | - Ian Nielsen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | | | - Yonglun Luo
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, BGI-Shenzhen, Shenzhen, China
| | - Karen Dybkaer
- Department of Hematology, Aalborg University Hospital, Aalborg, Denmark
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6
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Kuusanmäki H, Kytölä S, Vänttinen I, Ruokoranta T, Ranta A, Huuhtanen J, Suvela M, Parsons A, Holopainen A, Partanen A, Kuusisto MEL, Koskela S, Räty R, Itälä-Remes M, Västrik I, Dufva O, Siitonen S, Porkka K, Wennerberg K, Heckman CA, Ettala P, Pyörälä M, Rimpiläinen J, Siitonen T, Kontro M. Ex vivo venetoclax sensitivity testing predicts treatment response in acute myeloid leukemia. Haematologica 2023; 108:1768-1781. [PMID: 36519325 PMCID: PMC10316276 DOI: 10.3324/haematol.2022.281692] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 11/28/2022] [Indexed: 07/25/2023] Open
Abstract
The BCL-2 inhibitor venetoclax has revolutionized the treatment of acute myeloid leukemia (AML) in patients not benefiting from intensive chemotherapy. Nevertheless, treatment failure remains a challenge, and predictive markers are needed, particularly for relapsed or refractory AML. Ex vivo drug sensitivity testing may correlate with outcomes, but its prospective predictive value remains unexplored. Here we report the results of the first stage of the prospective phase II VenEx trial evaluating the utility and predictiveness of venetoclax sensitivity testing using different cell culture conditions and cell viability assays in patients receiving venetoclax-azacitidine. Participants with de novo AML ineligible for intensive chemotherapy, relapsed or refractory AML, or secondary AML were included. The primary endpoint was the treatment response in participants showing ex vivo sensitivity and the key secondary endpoints were the correlation of sensitivity with responses and survival. Venetoclax sensitivity testing was successful in 38/39 participants. Experimental conditions significantly influenced the predictive accuracy. Blast-specific venetoclax sensitivity measured in conditioned medium most accurately correlated with treatment outcomes; 88% of sensitive participants achieved a treatment response. The median survival was significantly longer for participants who were ex vivo-sensitive to venetoclax (14.6 months for venetoclax-sensitive patients vs. 3.5 for venetoclax-insensitive patients, P<0.001). This analysis illustrates the feasibility of integrating drug-response profiling into clinical practice and demonstrates excellent predictivity. This trial is registered with ClinicalTrials.gov identifier: NCT04267081.
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Affiliation(s)
- Heikki Kuusanmäki
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland; Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark; Foundation for the Finnish Cancer Institute, Helsinki
| | - Sari Kytölä
- Department of Hematology, Helsinki University Hospital Comprehensive Cancer Center, Helsinki
| | - Ida Vänttinen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki
| | - Tanja Ruokoranta
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki
| | - Amanda Ranta
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki
| | - Jani Huuhtanen
- Hematology Research Unit, University of Helsinki, Helsinki
| | - Minna Suvela
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki
| | - Alun Parsons
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki
| | | | - Anu Partanen
- Department of Medicine, Kuopio University Hospital, Kuopio
| | - Milla E L Kuusisto
- Department of Medicine, Oulu University Hospital, Oulu, Finland; Department of Hematology, University of Oulu, Oulu
| | - Sirpa Koskela
- Department of Internal Medicine, Tampere University Hospital, Tampere
| | - Riikka Räty
- Department of Hematology, Helsinki University Hospital Comprehensive Cancer Center, Helsinki
| | | | - Imre Västrik
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki
| | - Olli Dufva
- Hematology Research Unit, University of Helsinki, Helsinki
| | - Sanna Siitonen
- Department of Clinical Chemistry, University of Helsinki and Helsinki University Hospital
| | - Kimmo Porkka
- Department of Hematology, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland; Hematology Research Unit, University of Helsinki, Helsinki
| | - Krister Wennerberg
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen
| | - Caroline A Heckman
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki
| | - Pia Ettala
- Department of Clinical Hematology, Turku University Hospital, Turku
| | - Marja Pyörälä
- Department of Medicine, Kuopio University Hospital, Kuopio
| | | | - Timo Siitonen
- Department of Medicine, Oulu University Hospital, Oulu
| | - Mika Kontro
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland; Foundation for the Finnish Cancer Institute, Helsinki, Finland; Department of Hematology, Helsinki University Hospital Comprehensive Cancer Center, Helsinki.
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7
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Tislevoll BS, Hellesøy M, Fagerholt OHE, Gullaksen SE, Srivastava A, Birkeland E, Kleftogiannis D, Ayuda-Durán P, Piechaczyk L, Tadele DS, Skavland J, Panagiotis B, Hovland R, Andresen V, Seternes OM, Tvedt THA, Aghaeepour N, Gavasso S, Porkka K, Jonassen I, Fløisand Y, Enserink J, Blaser N, Gjertsen BT. Early response evaluation by single cell signaling profiling in acute myeloid leukemia. Nat Commun 2023; 14:115. [PMID: 36611026 PMCID: PMC9825407 DOI: 10.1038/s41467-022-35624-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 12/13/2022] [Indexed: 01/09/2023] Open
Abstract
Aberrant pro-survival signaling is a hallmark of cancer cells, but the response to chemotherapy is poorly understood. In this study, we investigate the initial signaling response to standard induction chemotherapy in a cohort of 32 acute myeloid leukemia (AML) patients, using 36-dimensional mass cytometry. Through supervised and unsupervised machine learning approaches, we find that reduction of extracellular-signal-regulated kinase (ERK) 1/2 and p38 mitogen-activated protein kinase (MAPK) phosphorylation in the myeloid cell compartment 24 h post-chemotherapy is a significant predictor of patient 5-year overall survival in this cohort. Validation by RNA sequencing shows induction of MAPK target gene expression in patients with high phospho-ERK1/2 24 h post-chemotherapy, while proteomics confirm an increase of the p38 prime target MAPK activated protein kinase 2 (MAPKAPK2). In this study, we demonstrate that mass cytometry can be a valuable tool for early response evaluation in AML and elucidate the potential of functional signaling analyses in precision oncology diagnostics.
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Affiliation(s)
- Benedicte Sjo Tislevoll
- Centre for Cancer Biomarkers (CCBIO), Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Monica Hellesøy
- Department of Internal Medicine, Hematology Section, Haukeland University Hospital, Helse Bergen HF, Bergen, Norway
| | - Oda Helen Eck Fagerholt
- Centre for Cancer Biomarkers (CCBIO), Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Stein-Erik Gullaksen
- Department of Internal Medicine, Hematology Section, Haukeland University Hospital, Helse Bergen HF, Bergen, Norway
| | - Aashish Srivastava
- Genome Core Facility, Clinical Laboratory, K2 Haukeland University Hospital, Bergen, Norway
| | - Even Birkeland
- The Proteomics Facility of the University of Bergen (PROBE), University of Bergen, Bergen, Norway
| | - Dimitrios Kleftogiannis
- Centre for Cancer Biomarkers (CCBIO), Department of Clinical Science, University of Bergen, Bergen, Norway.,Centre for Cancer Biomarkers and Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Pilar Ayuda-Durán
- Department of Molecular Cell Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Montebello, 0379, Oslo, Norway.,Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, 0318, Oslo, Norway
| | - Laure Piechaczyk
- Department of Molecular Cell Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Montebello, 0379, Oslo, Norway.,Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, 0318, Oslo, Norway.,Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Dagim Shiferaw Tadele
- Department of Molecular Genetics, Division of Laboratory Medicine, Oslo University Hospital, Oslo, Norway.,Department of Translational Hematology and Oncology Research, Cleveland Clinic, OH, 44106, USA
| | - Jørn Skavland
- Centre for Cancer Biomarkers (CCBIO), Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Baliakas Panagiotis
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Randi Hovland
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - Vibeke Andresen
- Centre for Cancer Biomarkers (CCBIO), Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Ole Morten Seternes
- Department of Pharmacy, UiT-The Arctic University of Norway, 9037, Tromsø, Norway
| | | | - Nima Aghaeepour
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, 94121, USA.,Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94121, USA.,Department of Biomedical Informatics, Stanford University School of Medicine, Stanford, CA, 94121, USA
| | - Sonia Gavasso
- Centre for Cancer Biomarkers (CCBIO), Department of Clinical Science, University of Bergen, Bergen, Norway.,Centre for Clinical Treatment Research (NeuroSysMed), Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Kimmo Porkka
- Department of Hematology, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
| | - Inge Jonassen
- Centre for Cancer Biomarkers and Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Yngvar Fløisand
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, 0318, Oslo, Norway.,Department of Hematology, Oslo University Hospital, Oslo, Norway
| | - Jorrit Enserink
- Department of Molecular Cell Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Montebello, 0379, Oslo, Norway.,Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, 0318, Oslo, Norway.,Section for Biochemistry and Molecular Biology, Faculty of Mathematics and Natural Sciences, University of Oslo, 0037, Oslo, Norway
| | - Nello Blaser
- Department of Informatics, University of Bergen, Bergen, Norway.
| | - Bjørn Tore Gjertsen
- Centre for Cancer Biomarkers (CCBIO), Department of Clinical Science, University of Bergen, Bergen, Norway. .,Department of Internal Medicine, Hematology Section, Haukeland University Hospital, Helse Bergen HF, Bergen, Norway.
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8
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Adashek JJ, Subbiah V, Westphalen CB, Naing A, Kato S, Kurzrock R. Cancer: slaying the nine-headed Hydra. Ann Oncol 2023; 34:61-69. [PMID: 35931318 PMCID: PMC10923524 DOI: 10.1016/j.annonc.2022.07.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 07/17/2022] [Accepted: 07/22/2022] [Indexed: 02/03/2023] Open
Abstract
Modern medicine continues to evolve, and the treatment armamentarium for various diseases grows more individualized across a breadth of medical disciplines. Cure rates for infectious diseases that were previously pan-fatal approach 100% because of the identification of the specific pathogen(s) involved and the use of appropriate combinations of drugs, where needed, to completely extinguish infection and hence prevent emergence of resistant strains. Similarly, with the assistance of technologies such as next-generation sequencing and immunomic analysis as part of the contemporary oncology armory, therapies can be tailored to each tumor. Importantly, molecular interrogation has revealed that metastatic cancers are distinct from each other and complex. Therefore, it is conceivable that rational personalized drug combinations will be needed to eradicate cancers, and eradication will be necessary to mitigate clonal evolution and resistance.
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Affiliation(s)
- J J Adashek
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins Hospital, Baltimore.
| | - V Subbiah
- The University of Texas MD Anderson Cancer Center, Houston, USA
| | - C B Westphalen
- Comprehensive Cancer Center Munich and Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
| | - A Naing
- The University of Texas MD Anderson Cancer Center, Houston, USA
| | - S Kato
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, Department of Medicine, University of California, San Diego
| | - R Kurzrock
- WIN Consortium, San Diego; MCW Cancer Center, Milwaukee; University of Nebraska, Omaha, USA.
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9
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Strachan DC, Gu CJ, Kita R, Anderson EK, Richardson MA, Yam G, Pimm G, Roselli J, Schweickert A, Terrell M, Rashid R, Gonzalez AK, Oviedo HH, Alozie MC, Ilangovan T, Marcogliese AN, Tada H, Santaguida MT, Stevens AM. Ex Vivo Drug Sensitivity Correlates with Clinical Response and Supports Personalized Therapy in Pediatric AML. Cancers (Basel) 2022; 14:cancers14246240. [PMID: 36551725 PMCID: PMC9777060 DOI: 10.3390/cancers14246240] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/01/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022] Open
Abstract
Acute myeloid leukemia (AML) is a heterogeneous disease that accounts for ~20% of all childhood leukemias, and more than 40% of children with AML relapse within three years of diagnosis. Although recent efforts have focused on developing a precise medicine-based approach towards treating AML in adults, there remains a critical gap in therapies designed specifically for children. Here, we present ex vivo drug sensitivity profiles for children with de novo AML using an automated flow cytometry platform. Fresh diagnostic blood or bone marrow aspirate samples were screened for sensitivity in response to 78 dose conditions by measuring the reduction in leukemic blasts relative to the control. In pediatric patients treated with conventional chemotherapy, comprising cytarabine, daunorubicin and etoposide (ADE), ex vivo drug sensitivity results correlated with minimal residual disease (r = 0.63) and one year relapse-free survival (r = 0.70; AUROC = 0.94). In the de novo ADE analysis cohort of 13 patients, AML cells showed greater sensitivity to bortezomib/panobinostat compared with ADE, and comparable sensitivity between venetoclax/azacitidine and ADE ex vivo. Two patients showed a differential response between ADE and bortezomib/panobinostat, thus supporting the incorporation of ex vivo drug sensitivity testing in clinical trials to further evaluate the predictive utility of this platform in children with AML.
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Affiliation(s)
| | | | | | | | | | - George Yam
- Notable Labs, Foster City, CA 94404, USA
| | | | | | | | - Maci Terrell
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Raushan Rashid
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alan K. Gonzalez
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hailey H. Oviedo
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Michelle C. Alozie
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tamilini Ilangovan
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | | | | | - Alexandra M. Stevens
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
- Correspondence:
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10
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Kimmerling RJ, Stevens MM, Olcum S, Minnah A, Vacha M, LaBella R, Ferri M, Wasserman SC, Fujii J, Shaheen Z, Sundaresan S, Ribadeneyra D, Jayabalan DS, Agte S, Aleman A, Criscitiello JA, Niesvizky R, Luskin MR, Parekh S, Rosenbaum CA, Tamrazi A, Reid CA. A pipeline for malignancy and therapy agnostic assessment of cancer drug response using cell mass measurements. Commun Biol 2022; 5:1295. [PMID: 36435843 PMCID: PMC9701192 DOI: 10.1038/s42003-022-04270-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 11/16/2022] [Indexed: 11/28/2022] Open
Abstract
Functional precision medicine offers a promising complement to genomics-based cancer therapy guidance by testing drug efficacy directly on a patient's tumor cells. Here, we describe a workflow that utilizes single-cell mass measurements with inline brightfield imaging and machine-learning based image classification to broaden the clinical utility of such functional testing for cancer. Using these image-curated mass measurements, we characterize mass response signals for 60 different drugs with various mechanisms of action across twelve different cell types, demonstrating an improved ability to detect response for several slow acting drugs as compared with standard cell viability assays. Furthermore, we use this workflow to assess drug responses for various primary tumor specimen formats including blood, bone marrow, fine needle aspirates (FNA), and malignant fluids, all with reports generated within two days and with results consistent with patient clinical responses. The combination of high-resolution measurement, broad drug and malignancy applicability, and rapid return of results offered by this workflow suggests that it is well-suited to performing clinically relevant functional assessment of cancer drug response.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Juanita Fujii
- Department of Clinical Research, Dignity Health, Sequoia Hospital, Redwood City, CA, USA
| | - Zayna Shaheen
- Department of Clinical Research, Dignity Health, Sequoia Hospital, Redwood City, CA, USA
| | - Srividya Sundaresan
- Department of Clinical Research, Dignity Health, Sequoia Hospital, Redwood City, CA, USA
| | | | | | - Sarita Agte
- Department of Medicine, Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adolfo Aleman
- Department of Medicine, Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | | | - Marlise R Luskin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Samir Parekh
- Department of Medicine, Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Anobel Tamrazi
- Division of Vascular and Interventional Radiology, Palo Alto Medical Foundation, Redwood City, CA, USA
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11
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Jegatheeson S, Cannon C, Mansfield C, Devlin J, Roberts A. Sensitivity of canine hematological cancers to BH3 mimetics. J Vet Intern Med 2022; 37:236-246. [PMID: 36433867 PMCID: PMC9889650 DOI: 10.1111/jvim.16587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 11/08/2022] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Inhibition of antiapoptotic B-cell lymphoma 2 (BCL2) proteins by small molecule Bcl-2 homology 3 (BH3) mimetics causes rapid induction of apoptosis of human hematological cancers in vitro and in vivo. OBJECTIVES Assess in vitro sensitivity of non-neoplastic lymphocytes and primary hematological cancer cells from dogs to venetoclax (VEN) or the dual BCL2/ B-cell lymphoma-extra-large (BCLxL) inhibitor, navitoclax (NAV), and evaluate the association between BCL2 protein expression and VEN sensitivity. ANIMALS Nine client-owned dogs without cancer and 18 client-owned dogs with hematological cancer. METHODS Prospective, nonrandomized noncontrolled study. Lymphocytes isolated from peripheral blood, lymph node, or bone marrow from dogs were incubated with BH3 mimetics for 24 hours. Viable cells were counted using flow cytometry and half maximal effective concentration (EC50 ) was calculated. BCL2 protein from whole cell lysates was assessed via immunoblots. RESULTS Nodal B and T lymphocytes were more sensitive to VEN than circulating lymphocytes (P = .02). Neoplastic T lymphocytes were sensitive to VEN (mean EC50 ± SD = 0.023 ± 0.018 μM), whereas most non-indolent B cell cancers were resistant to killing by VEN (mean EC50 ± SD = 288 ± 700 μM). Unclassified leukemias showed variable sensitivity to VEN (mean EC50 ± SD = 0.49 ± 0.66 μM). Detection of BCL2 protein was not associated with VEN sensitivity. CONCLUSION AND CLINICAL IMPORTANCE Neoplastic canine T lymphocytes are sensitive to VEN in vitro. Quantification of BCL2 protein alone is insufficient to predict sensitivity to VEN.
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Affiliation(s)
- Selvi Jegatheeson
- Faculty of Veterinary and Agricultural SciencesThe University of MelbourneWerribeeVictoriaAustralia,Blood Cells and Blood Cancer DivisionThe Walter and Eliza Hall Institute of Medical ResearchParkvilleVictoriaAustralia
| | - Claire Cannon
- Faculty of Veterinary and Agricultural SciencesThe University of MelbourneWerribeeVictoriaAustralia,Present address:
Veterinary Referral HospitalDandenongVictoriaAustralia
| | - Caroline Mansfield
- Faculty of Veterinary and Agricultural SciencesThe University of MelbourneWerribeeVictoriaAustralia
| | - Joanne Devlin
- Faculty of Veterinary and Agricultural SciencesThe University of MelbourneWerribeeVictoriaAustralia
| | - Andrew Roberts
- Blood Cells and Blood Cancer DivisionThe Walter and Eliza Hall Institute of Medical ResearchParkvilleVictoriaAustralia
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12
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Goh J, De Mel S, Hoppe MM, Mohd Abdul Rashid MB, Zhang XY, Jaynes P, Ka Yan Ng E, Rahmat NDB, Jayalakshmi, Liu CX, Poon L, Chan E, Lee J, Chee YL, Koh LP, Tan LK, Soh TG, Yuen YC, Loi HY, Ng SB, Goh X, Eu D, Loh S, Ng S, Tan D, Cheah DMZ, Pang WL, Huang D, Ong SY, Nagarajan C, Chan JY, Ha JCH, Khoo LP, Somasundaram N, Tang T, Ong CK, Chng WJ, Lim ST, Chow EK, Jeyasekharan AD. An ex vivo platform to guide drug combination treatment in relapsed/refractory lymphoma. Sci Transl Med 2022; 14:eabn7824. [PMID: 36260690 DOI: 10.1126/scitranslmed.abn7824] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Although combination therapy is the standard of care for relapsed/refractory non-Hodgkin's lymphoma (RR-NHL), combination treatment chosen for an individual patient is empirical, and response rates remain poor in individuals with chemotherapy-resistant disease. Here, we evaluate an experimental-analytic method, quadratic phenotypic optimization platform (QPOP), for prediction of patient-specific drug combination efficacy from a limited quantity of biopsied tumor samples. In this prospective study, we enrolled 71 patients with RR-NHL (39 B cell NHL and 32 NK/T cell NHL) with a median of two prior lines of treatment, at two academic hospitals in Singapore from November 2017 to August 2021. Fresh biopsies underwent ex vivo testing using a panel of 12 drugs with known efficacy against NHL to identify effective single and combination treatments. Individualized QPOP reports were generated for 67 of 75 patient samples, with a median turnaround time of 6 days from sample collection to report generation. Doublet drug combinations containing copanlisib or romidepsin were most effective against B cell NHL and NK/T cell NHL samples, respectively. Off-label QPOP-guided therapy offered at physician discretion in the absence of standard options (n = 17) resulted in five complete responses. Among patients with more than two prior lines of therapy, the rates of progressive disease were lower with QPOP-guided treatments than with conventional chemotherapy. Overall, this study shows that the identification of patient-specific drug combinations through ex vivo analysis was achievable for RR-NHL in a clinically applicable time frame. These data provide the basis for a prospective clinical trial evaluating ex vivo-guided combination therapy in RR-NHL.
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Affiliation(s)
- Jasmine Goh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Sanjay De Mel
- NUS Center for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University Singapore, Singapore 117599, Singapore.,Department of Haematology-Oncology, National University Cancer Institute, Singapore, National University Health System, Singapore 119074, Singapore
| | - Michal M Hoppe
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | | | - Xi Yun Zhang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Patrick Jaynes
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Esther Ka Yan Ng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | | | - Jayalakshmi
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Clementine Xin Liu
- Department of Haematology-Oncology, National University Cancer Institute, Singapore, National University Health System, Singapore 119074, Singapore
| | - Limei Poon
- NUS Center for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University Singapore, Singapore 117599, Singapore.,Department of Haematology-Oncology, National University Cancer Institute, Singapore, National University Health System, Singapore 119074, Singapore
| | - Esther Chan
- NUS Center for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University Singapore, Singapore 117599, Singapore.,Department of Haematology-Oncology, National University Cancer Institute, Singapore, National University Health System, Singapore 119074, Singapore
| | - Joanne Lee
- NUS Center for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University Singapore, Singapore 117599, Singapore.,Department of Haematology-Oncology, National University Cancer Institute, Singapore, National University Health System, Singapore 119074, Singapore
| | - Yen Lin Chee
- NUS Center for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University Singapore, Singapore 117599, Singapore.,Department of Haematology-Oncology, National University Cancer Institute, Singapore, National University Health System, Singapore 119074, Singapore
| | - Liang Piu Koh
- Department of Haematology-Oncology, National University Cancer Institute, Singapore, National University Health System, Singapore 119074, Singapore
| | - Lip Kun Tan
- Department of Laboratory Medicine, National University Hospital, Singapore 119074, Singapore
| | - Teck Guan Soh
- Department of Laboratory Medicine, National University Hospital, Singapore 119074, Singapore
| | - Yi Ching Yuen
- Department of Pharmacy, National University Health System, Singapore 119074, Singapore
| | - Hoi-Yin Loi
- Department of Diagnostic Imaging, National University Hospital, Singapore 119074, Singapore
| | - Siok-Bian Ng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore.,NUS Center for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University Singapore, Singapore 117599, Singapore.,Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Xueying Goh
- Department of Otolaryngology, National University Hospital, Singapore 119074, Singapore
| | - Donovan Eu
- Department of Otolaryngology, National University Hospital, Singapore 119074, Singapore
| | - Stanley Loh
- Department of Diagnostic Imaging, National University Hospital, Singapore 119074, Singapore
| | - Sheldon Ng
- Department of Diagnostic Imaging, National University Hospital, Singapore 119074, Singapore
| | - Daryl Tan
- Mount Elizabeth Novena Hospital, Singapore 329563, Singapore.,Department of Haematology, Singapore General Hospital, Singapore 169608, Singapore
| | - Daryl Ming Zhe Cheah
- Lymphoma Genomic Translational Research Laboratory, Division of Cellular and Molecular Research, National Cancer Centre Singapore, Singapore 169610, Singapore
| | - Wan Lu Pang
- Lymphoma Genomic Translational Research Laboratory, Division of Cellular and Molecular Research, National Cancer Centre Singapore, Singapore 169610, Singapore
| | - Dachuan Huang
- Lymphoma Genomic Translational Research Laboratory, Division of Cellular and Molecular Research, National Cancer Centre Singapore, Singapore 169610, Singapore
| | - Shin Yeu Ong
- Department of Haematology, Singapore General Hospital, Singapore 169608, Singapore
| | | | - Jason Yongsheng Chan
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore 169610, Singapore.,SingHealth Duke-NUS Blood Cancer Centre, Singapore 168582, Singapore
| | - Jeslin Chian Hung Ha
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore 169610, Singapore
| | - Lay Poh Khoo
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore 169610, Singapore
| | - Nagavalli Somasundaram
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore 169610, Singapore
| | - Tiffany Tang
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore 169610, Singapore
| | - Choon Kiat Ong
- Lymphoma Genomic Translational Research Laboratory, Division of Cellular and Molecular Research, National Cancer Centre Singapore, Singapore 169610, Singapore.,Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore.,Genome Institute of Singapore, A*STAR, Singapore 138672, Singapore
| | - Wee-Joo Chng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore.,NUS Center for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University Singapore, Singapore 117599, Singapore.,Department of Haematology-Oncology, National University Cancer Institute, Singapore, National University Health System, Singapore 119074, Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Soon Thye Lim
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore 169610, Singapore.,SingHealth Duke-NUS Blood Cancer Centre, Singapore 168582, Singapore.,Office of Education, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Edward K Chow
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore.,NUS Center for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University Singapore, Singapore 117599, Singapore.,Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore.,N.1 Institute for Health, National University of Singapore, Singapore 117456, Singapore.,Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Anand D Jeyasekharan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore.,NUS Center for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University Singapore, Singapore 117599, Singapore.,Department of Haematology-Oncology, National University Cancer Institute, Singapore, National University Health System, Singapore 119074, Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
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13
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Free T. Investigating myeloid cells? Go with the flow. Biotechniques 2022; 73:163-165. [PMID: 36205120 DOI: 10.2144/btn-2022-0099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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14
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Flobak Å, Skånland SS, Hovig E, Taskén K, Russnes HG. Functional precision cancer medicine: drug sensitivity screening enabled by cell culture models. Trends Pharmacol Sci 2022; 43:973-985. [PMID: 36163057 DOI: 10.1016/j.tips.2022.08.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 08/20/2022] [Accepted: 08/22/2022] [Indexed: 10/31/2022]
Abstract
Functional precision medicine is a new, emerging area that can guide cancer treatment by capturing information from direct perturbations of tumor-derived, living cells, such as by drug sensitivity screening. Precision cancer medicine as currently implemented in clinical practice has been driven by genomics, and current molecular tumor boards rely extensively on genomic characterization to advise on therapeutic interventions. However, genomic biomarkers can only guide treatment decisions for a fraction of the patients. In this review we provide an overview of the current state of functional precision medicine, highlight advances for drug-sensitivity screening enabled by cell culture models, and discuss how artificial intelligence (AI) can be coupled to functional precision medicine to guide patient stratification.
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Affiliation(s)
- Åsmund Flobak
- The Cancer Clinic, St. Olav University Hospital, Trondheim, Norway; Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Sigrid S Skånland
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway; K.G. Jebsen Centre for B Cell Malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Eivind Hovig
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway; Department of Informatics, Centre for Bioinformatics, University of Oslo, Oslo, Norway
| | - Kjetil Taskén
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway; K.G. Jebsen Centre for B Cell Malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
| | - Hege G Russnes
- Department of Pathology, Oslo University Hospital, Oslo, Norway; Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway; Institute of Clinical Medicine, University of Oslo, Oslo, Norway
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15
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Xiang W, Lam YH, Periyasamy G, Chuah C. Application of High Throughput Technologies in the Development of Acute Myeloid Leukemia Therapy: Challenges and Progress. Int J Mol Sci 2022; 23:ijms23052863. [PMID: 35270002 PMCID: PMC8910862 DOI: 10.3390/ijms23052863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/26/2022] [Accepted: 02/28/2022] [Indexed: 11/27/2022] Open
Abstract
Acute myeloid leukemia (AML) is a complex hematological malignancy characterized by extensive heterogeneity in genetics, response to therapy and long-term outcomes, making it a prototype example of development for personalized medicine. Given the accessibility to hematologic malignancy patient samples and recent advances in high-throughput technologies, large amounts of biological data that are clinically relevant for diagnosis, risk stratification and targeted drug development have been generated. Recent studies highlight the potential of implementing genomic-based and phenotypic-based screens in clinics to improve survival in patients with refractory AML. In this review, we will discuss successful applications as well as challenges of most up-to-date high-throughput technologies, including artificial intelligence (AI) approaches, in the development of personalized medicine for AML, and recent clinical studies for evaluating the utility of integrating genomics-guided and drug sensitivity testing-guided treatment approaches for AML patients.
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Affiliation(s)
- Wei Xiang
- Department of Haematology, Singapore General Hospital, Singapore 169608, Singapore; (W.X.); (Y.H.L.)
| | - Yi Hui Lam
- Department of Haematology, Singapore General Hospital, Singapore 169608, Singapore; (W.X.); (Y.H.L.)
| | - Giridharan Periyasamy
- High Throughput Phenomics Platform, Experimental Drug Development Centre, Agency for Science, Technology and Research (A*STAR), Singapore 139632, Singapore;
| | - Charles Chuah
- Department of Haematology, Singapore General Hospital, Singapore 169608, Singapore; (W.X.); (Y.H.L.)
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore 169857, Singapore
- Correspondence:
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16
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Branstrom A, Cao L, Furia B, Trotta C, Santaguida M, Graci JD, Colacino JM, Ray B, Li W, Sheedy J, Mollin A, Yeh S, Kong R, Sheridan R, Baird JD, O'Keefe K, Spiegel R, Goodwin E, Keating S, Weetall M. Emvododstat, a Potent Dihydroorotate Dehydrogenase Inhibitor, Is Effective in Preclinical Models of Acute Myeloid Leukemia. Front Oncol 2022; 12:832816. [PMID: 35223511 PMCID: PMC8864546 DOI: 10.3389/fonc.2022.832816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 01/20/2022] [Indexed: 11/13/2022] Open
Abstract
Blocking the pyrimidine nucleotide de novo synthesis pathway by inhibiting dihydroorotate dehydrogenase (DHODH) results in the cell cycle arrest and/or differentiation of rapidly proliferating cells including activated lymphocytes, cancer cells, or virally infected cells. Emvododstat (PTC299) is an orally bioavailable small molecule that inhibits DHODH. We evaluated the potential for emvododstat to inhibit the progression of acute myeloid leukemia (AML) using several in vitro and in vivo models of the disease. Broad potent activity was demonstrated against multiple AML cell lines, AML blasts cultured ex vivo from patient blood samples, and AML tumor models including patient-derived xenograft models. Emvododstat induced differentiation, cytotoxicity, or both in primary AML patient blasts cultured ex vivo with 8 of 10 samples showing sensitivity. AML cells with diverse driver mutations were sensitive, suggesting the potential of emvododstat for broad therapeutic application. AML cell lines that are not sensitive to emvododstat are likely to be more reliant on the salvage pathway than on de novo synthesis of pyrimidine nucleotides. Pharmacokinetic experiments in rhesus monkeys demonstrated that emvododstat levels rose rapidly after oral administration, peaking about 2 hours post-dosing. This was associated with an increase in the levels of dihydroorotate (DHO), the substrate for DHODH, within 2 hours of dosing indicating that DHODH inhibition is rapid. DHO levels declined as drug levels declined, consistent with the reversibility of DHODH inhibition by emvododstat. These preclinical findings provide a rationale for clinical evaluation of emvododstat in an ongoing Phase 1 study of patients with relapsed/refractory acute leukemias.
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Affiliation(s)
- Arthur Branstrom
- Research, PTC Therapeutics, Inc., South Plainfield, NJ, United States
| | - Liangxian Cao
- Research, PTC Therapeutics, Inc., South Plainfield, NJ, United States
| | - Bansri Furia
- Research, PTC Therapeutics, Inc., South Plainfield, NJ, United States
| | | | | | - Jason D Graci
- Research, PTC Therapeutics, Inc., South Plainfield, NJ, United States
| | - Joseph M Colacino
- Research, PTC Therapeutics, Inc., South Plainfield, NJ, United States
| | - Balmiki Ray
- Research, PTC Therapeutics, Inc., South Plainfield, NJ, United States
| | - Wencheng Li
- Research, PTC Therapeutics, Inc., South Plainfield, NJ, United States
| | - Josephine Sheedy
- Research, PTC Therapeutics, Inc., South Plainfield, NJ, United States
| | - Anna Mollin
- Research, PTC Therapeutics, Inc., South Plainfield, NJ, United States
| | - Shirley Yeh
- Research, PTC Therapeutics, Inc., South Plainfield, NJ, United States
| | - Ronald Kong
- Research, PTC Therapeutics, Inc., South Plainfield, NJ, United States
| | | | - John D Baird
- Clinical, PTC Therapeutics, Inc., South Plainfield, NJ, United States
| | - Kylie O'Keefe
- Commercial, PTC Therapeutics, Inc., South Plainfield, NJ, United States
| | - Robert Spiegel
- Research, PTC Therapeutics, Inc., South Plainfield, NJ, United States
| | - Elizabeth Goodwin
- Scientific Writing, PTC Therapeutics, Inc., South Plainfield, NJ, United States
| | - Suzanne Keating
- Scientific Writing, PTC Therapeutics, Inc., South Plainfield, NJ, United States
| | - Marla Weetall
- Research, PTC Therapeutics, Inc., South Plainfield, NJ, United States
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17
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Eaton A, Wong V, Schiff D, Anderson E, Ding H, Capparelli EV, Determan D, Kuo DJ. Tumor Genomic Profiling and Ex Vivo Drug Sensitivity Testing for Pediatric Leukemia and Lymphoma Patients. J Pediatr Pharmacol Ther 2022; 27:123-131. [DOI: 10.5863/1551-6776-27.2.123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 07/04/2021] [Indexed: 11/11/2022]
Abstract
OBJECTIVE
To describe the frequency of use of tumor genomic profiling and functional ex vivo drug sensitivity testing in pediatric patients with hematologic malignancies at our institution, and to determine how the results affected treatment selection.
METHODS
A retrospective chart review was conducted to analyze the frequency of tumor genomic profiling and functional drug sensitivity screening in our institution in pediatric patients with hematologic malignancies and to ask if the results were used to direct treatment. A case series of patients for whom these testing recommendations resulted in therapeutic interventions is reported.
RESULTS
Thirty-three patients underwent tumor genomic profiling assays, functional ex vivo testing, or both. Nineteen patients (58%) had genomic profiling assays performed alone, 3 (9%) had functional ex vivo testing performed alone, and 11 (33%) had both tests performed. Twenty-one (64%) patients had potentially actionable mutations detected by the genomic profiling assay. Seven (21%) patients received at least 1 chemotherapeutic agent in accordance with the tumor genomic profiling or functional ex vivo drug sensitivity testing results. Three (43%) of the 7 patients who were treated with testing directed therapy had a favorable treatment response (PR or CR) to treatments selected based upon results of genomic or functional ex vivo testing.
CONCLUSIONS
This retrospective case series demonstrates that precision medicine techniques such as genomic profiling and drug sensitivity testing can positively inform treatment selection in pediatric patients with relapsed or refractory leukemia and lymphoma.
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Affiliation(s)
- Aubrie Eaton
- Department of Pharmacy (AE, DD), Rady Children's Hospital, San Diego, San Diego, CA
| | - Victor Wong
- Department of Pediatrics, Division of Hematology-Oncology (VW, DS, EA, HD, DJK), University of California San Diego, La Jolla, CA/Rady Children's Hospital, San Diego, San Diego, CA
| | - Deborah Schiff
- Department of Pediatrics, Division of Hematology-Oncology (VW, DS, EA, HD, DJK), University of California San Diego, La Jolla, CA/Rady Children's Hospital, San Diego, San Diego, CA
| | - Eric Anderson
- Department of Pediatrics, Division of Hematology-Oncology (VW, DS, EA, HD, DJK), University of California San Diego, La Jolla, CA/Rady Children's Hospital, San Diego, San Diego, CA
| | - Hilda Ding
- Department of Pediatrics, Division of Hematology-Oncology (VW, DS, EA, HD, DJK), University of California San Diego, La Jolla, CA/Rady Children's Hospital, San Diego, San Diego, CA
| | - Edmund V. Capparelli
- Department of Pediatrics and Skaggs School of Pharmacy and Pharmaceutical Sciences (EVC), University of California San Diego, La Jolla, CA
| | - Deb Determan
- Department of Pharmacy (AE, DD), Rady Children's Hospital, San Diego, San Diego, CA
| | - Dennis John Kuo
- Department of Pediatrics, Division of Hematology-Oncology (VW, DS, EA, HD, DJK), University of California San Diego, La Jolla, CA/Rady Children's Hospital, San Diego, San Diego, CA
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18
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Malani D, Kumar A, Brück O, Kontro M, Yadav B, Hellesøy M, Kuusanmäki H, Dufva O, Kankainen M, Eldfors S, Potdar S, Saarela J, Turunen L, Parsons A, Västrik I, Kivinen K, Saarela J, Räty R, Lehto M, Wolf M, Gjertsen BT, Mustjoki S, Aittokallio T, Wennerberg K, Heckman CA, Kallioniemi O, Porkka K. Implementing a Functional Precision Medicine Tumor Board for Acute Myeloid Leukemia. Cancer Discov 2022; 12:388-401. [PMID: 34789538 PMCID: PMC9762335 DOI: 10.1158/2159-8290.cd-21-0410] [Citation(s) in RCA: 65] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 10/14/2021] [Accepted: 11/11/2021] [Indexed: 01/07/2023]
Abstract
We generated ex vivo drug-response and multiomics profiling data for a prospective series of 252 samples from 186 patients with acute myeloid leukemia (AML). A functional precision medicine tumor board (FPMTB) integrated clinical, molecular, and functional data for application in clinical treatment decisions. Actionable drugs were found for 97% of patients with AML, and the recommendations were clinically implemented in 37 relapsed or refractory patients. We report a 59% objective response rate for the individually tailored therapies, including 13 complete responses, as well as bridging five patients with AML to allogeneic hematopoietic stem cell transplantation. Data integration across all cases enabled the identification of drug response biomarkers, such as the association of IL15 overexpression with resistance to FLT3 inhibitors. Integration of molecular profiling and large-scale drug response data across many patients will enable continuous improvement of the FPMTB recommendations, providing a paradigm for individualized implementation of functional precision cancer medicine. SIGNIFICANCE: Oncogenomics data can guide clinical treatment decisions, but often such data are neither actionable nor predictive. Functional ex vivo drug testing contributes significant additional, clinically actionable therapeutic insights for individual patients with AML. Such data can be generated in four days, enabling rapid translation through FPMTB.See related commentary by Letai, p. 290.This article is highlighted in the In This Issue feature, p. 275.
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Affiliation(s)
- Disha Malani
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Ashwini Kumar
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Oscar Brück
- Hematology Research Unit Helsinki, University of Helsinki, and Helsinki University Hospital Comprehensive Cancer Center, Department of Hematology, Helsinki, Finland.,Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland.,iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Mika Kontro
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland.,Hematology Research Unit Helsinki, University of Helsinki, and Helsinki University Hospital Comprehensive Cancer Center, Department of Hematology, Helsinki, Finland
| | - Bhagwan Yadav
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland.,Hematology Research Unit Helsinki, University of Helsinki, and Helsinki University Hospital Comprehensive Cancer Center, Department of Hematology, Helsinki, Finland
| | - Monica Hellesøy
- Department of Medicine, Hematology Section, Haukeland University Hospital, Bergen, Norway.,Center for Cancer Biomarkers (CCBIO), Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Heikki Kuusanmäki
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland.,Biotech Research & Innovation Centre (BRIC) and Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, Copenhagen, Denmark
| | - Olli Dufva
- Hematology Research Unit Helsinki, University of Helsinki, and Helsinki University Hospital Comprehensive Cancer Center, Department of Hematology, Helsinki, Finland.,Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
| | - Matti Kankainen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland.,Hematology Research Unit Helsinki, University of Helsinki, and Helsinki University Hospital Comprehensive Cancer Center, Department of Hematology, Helsinki, Finland.,Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland.,iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Samuli Eldfors
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland.,Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, Massachusetts, USA
| | - Swapnil Potdar
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Jani Saarela
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Laura Turunen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Alun Parsons
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Imre Västrik
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Katja Kivinen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Janna Saarela
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland.,Centre for Molecular Medicine Norway, NCMM, University of Oslo, Oslo, Norway
| | - Riikka Räty
- Hematology Research Unit Helsinki, University of Helsinki, and Helsinki University Hospital Comprehensive Cancer Center, Department of Hematology, Helsinki, Finland
| | - Minna Lehto
- Hematology Research Unit Helsinki, University of Helsinki, and Helsinki University Hospital Comprehensive Cancer Center, Department of Hematology, Helsinki, Finland
| | - Maija Wolf
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Bjorn Tore Gjertsen
- Department of Medicine, Hematology Section, Haukeland University Hospital, Bergen, Norway.,Center for Cancer Biomarkers (CCBIO), Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Satu Mustjoki
- Hematology Research Unit Helsinki, University of Helsinki, and Helsinki University Hospital Comprehensive Cancer Center, Department of Hematology, Helsinki, Finland.,Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland.,iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Tero Aittokallio
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland.,Institute for Cancer Research, Oslo University Hospital, and Oslo Centre for Biostatistics and Epidemiology, University of Oslo, Norway
| | - Krister Wennerberg
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland.,Biotech Research & Innovation Centre (BRIC) and Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, Copenhagen, Denmark
| | - Caroline A. Heckman
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland.,iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Olli Kallioniemi
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland.,iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland.,Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, Solna, Sweden.,Corresponding Authors: Kimmo Porkka, Helsinki University Hospital Comprehensive Cancer Center and Hematology Research Unit Helsinki, University of Helsinki, P.O. Box 372, FIN-00029 HUCH, Helsinki, Finland. Phone: 358-50-427-0192; Fax: 358-9-471-72351; E-mail: ; and Olli Kallioniemi, Molecular Precision Medicine, Department of Oncology and Pathology, Karolinska Institutet, Box 1031, Solna 171 21, Sweden. Phone: 46-70-7753642; E-mail:
| | - Kimmo Porkka
- Hematology Research Unit Helsinki, University of Helsinki, and Helsinki University Hospital Comprehensive Cancer Center, Department of Hematology, Helsinki, Finland.,iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland.,Corresponding Authors: Kimmo Porkka, Helsinki University Hospital Comprehensive Cancer Center and Hematology Research Unit Helsinki, University of Helsinki, P.O. Box 372, FIN-00029 HUCH, Helsinki, Finland. Phone: 358-50-427-0192; Fax: 358-9-471-72351; E-mail: ; and Olli Kallioniemi, Molecular Precision Medicine, Department of Oncology and Pathology, Karolinska Institutet, Box 1031, Solna 171 21, Sweden. Phone: 46-70-7753642; E-mail:
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19
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Ianevski A, Lahtela J, Javarappa KK, Sergeev P, Ghimire BR, Gautam P, Vähä-Koskela M, Turunen L, Linnavirta N, Kuusanmäki H, Kontro M, Porkka K, Heckman CA, Mattila P, Wennerberg K, Giri AK, Aittokallio T. Patient-tailored design for selective co-inhibition of leukemic cell subpopulations. SCIENCE ADVANCES 2021; 7:eabe4038. [PMID: 33608276 PMCID: PMC7895436 DOI: 10.1126/sciadv.abe4038] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 01/08/2021] [Indexed: 06/12/2023]
Abstract
The extensive drug resistance requires rational approaches to design personalized combinatorial treatments that exploit patient-specific therapeutic vulnerabilities to selectively target disease-driving cell subpopulations. To solve the combinatorial explosion challenge, we implemented an effective machine learning approach that prioritizes patient-customized drug combinations with a desired synergy-efficacy-toxicity balance by combining single-cell RNA sequencing with ex vivo single-agent testing in scarce patient-derived primary cells. When applied to two diagnostic and two refractory acute myeloid leukemia (AML) patient cases, each with a different genetic background, we accurately predicted patient-specific combinations that not only resulted in synergistic cancer cell co-inhibition but also were capable of targeting specific AML cell subpopulations that emerge in differing stages of disease pathogenesis or treatment regimens. Our functional precision oncology approach provides an unbiased means for systematic identification of personalized combinatorial regimens that selectively co-inhibit leukemic cells while avoiding inhibition of nonmalignant cells, thereby increasing their likelihood for clinical translation.
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Affiliation(s)
- Aleksandr Ianevski
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Helsinki Institute for Information Technology (HIIT), Department of Computer Science, Aalto University, Espoo, Finland
| | - Jenni Lahtela
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Komal K Javarappa
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Philipp Sergeev
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Bishwa R Ghimire
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Prson Gautam
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Markus Vähä-Koskela
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Laura Turunen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Nora Linnavirta
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Heikki Kuusanmäki
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Biotech Research and Innovation Centre (BRIC) and Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, Copenhagen, Denmark
- Department of Hematology, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
| | - Mika Kontro
- Department of Hematology, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
| | - Kimmo Porkka
- Helsinki University Hospital Comprehensive Cancer Center, Hematology Research Unit Helsinki, iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Caroline A Heckman
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Pirkko Mattila
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Krister Wennerberg
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland.
- Biotech Research and Innovation Centre (BRIC) and Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, Copenhagen, Denmark
| | - Anil K Giri
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland.
| | - Tero Aittokallio
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland.
- Helsinki Institute for Information Technology (HIIT), Department of Computer Science, Aalto University, Espoo, Finland
- Institute for Cancer Research, Department of Cancer Genetics, Oslo University Hospital, Oslo, Norway
- Centre for Biostatistics and Epidemiology (OCBE), Faculty of Medicine, University of Oslo, Oslo, Norway
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