1
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Futran AS, Lu T, Amberg-Johnson K, Xu J, Yang X, He S, Boyce S, Bell JA, Pelletier R, Suzuki T, Huang X, Qian H, Fang L, Xing L, Xu Z, Kurtz SE, Tyner JW, Tang W, Guo T, Akinsanya K, Madge D, Jensen KK. Ubiquitin-specific protease 7 inhibitors reveal a differentiated mechanism of p53-driven anti-cancer activity. iScience 2024; 27:109693. [PMID: 38689642 PMCID: PMC11059122 DOI: 10.1016/j.isci.2024.109693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/11/2024] [Accepted: 04/05/2024] [Indexed: 05/02/2024] Open
Abstract
The USP7 deubiquitinase regulates proteins involved in the cell cycle, DNA repair, and epigenetics and has been implicated in cancer progression. USP7 inhibition has been pursued for the development of anti-cancer therapies. Here, we describe the discovery of potent and specific USP7 inhibitors exemplified by FX1-5303. FX1-5303 was used as a chemical probe to study the USP7-mediated regulation of p53 signaling in cells. It demonstrates mechanistic differences compared to MDM2 antagonists, a related class of anti-tumor agents that act along the same pathway. FX1-5303 synergizes with the clinically approved BCL2 inhibitor venetoclax in acute myeloid leukemia (AML) cell lines and ex vivo patient samples and leads to strong tumor growth inhibition in in vivo mouse xenograft models of multiple myeloma and AML. This work introduces new USP7 inhibitors, differentiates their mechanism of action from MDM2 inhibition, and identifies specific opportunities for their use in the treatment of AML.
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Affiliation(s)
- Alan S. Futran
- Schrödinger, 1540 Broadway 24th Floor, New York, NY, USA
| | - Tao Lu
- WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | | | - Jiayi Xu
- Schrödinger, 1540 Broadway 24th Floor, New York, NY, USA
| | - Xiaoxiao Yang
- WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Saidi He
- WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Sarah Boyce
- Schrödinger, 1540 Broadway 24th Floor, New York, NY, USA
| | | | | | - Takao Suzuki
- WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Xianhai Huang
- Schrödinger, 1540 Broadway 24th Floor, New York, NY, USA
| | - Heng Qian
- WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Liping Fang
- WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Li Xing
- WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Zhaowu Xu
- WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Stephen E. Kurtz
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Jeffrey W. Tyner
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR, USA
| | - Wayne Tang
- Schrödinger, 1540 Broadway 24th Floor, New York, NY, USA
| | - Tao Guo
- WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | | | - David Madge
- WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
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2
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Modak RV, de Oliveira Rebola KG, McClatchy J, Mohammadhosseini M, Damnernsawad A, Kurtz SE, Eide CA, Wu G, Laderas T, Nechiporuk T, Gritsenko MA, Hansen JR, Hutchinson C, Gosline SJ, Piehowski P, Bottomly D, Short N, Rodland K, McWeeney SK, Tyner JW, Agarwal A. Targeting CCL2/CCR2 Signaling Overcomes MEK Inhibitor Resistance in Acute Myeloid Leukemia. Clin Cancer Res 2024; 30:2245-2259. [PMID: 38451486 PMCID: PMC11094423 DOI: 10.1158/1078-0432.ccr-23-2654] [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: 09/02/2023] [Revised: 12/29/2023] [Accepted: 03/05/2024] [Indexed: 03/08/2024]
Abstract
PURPOSE Emerging evidence underscores the critical role of extrinsic factors within the microenvironment in protecting leukemia cells from therapeutic interventions, driving disease progression, and promoting drug resistance in acute myeloid leukemia (AML). This finding emphasizes the need for the identification of targeted therapies that inhibit intrinsic and extrinsic signaling to overcome drug resistance in AML. EXPERIMENTAL DESIGN We performed a comprehensive analysis utilizing a cohort of ∼300 AML patient samples. This analysis encompassed the evaluation of secreted cytokines/growth factors, gene expression, and ex vivo drug sensitivity to small molecules. Our investigation pinpointed a notable association between elevated levels of CCL2 and diminished sensitivity to the MEK inhibitors (MEKi). We validated this association through loss-of-function and pharmacologic inhibition studies. Further, we deployed global phosphoproteomics and CRISPR/Cas9 screening to identify the mechanism of CCR2-mediated MEKi resistance in AML. RESULTS Our multifaceted analysis unveiled that CCL2 activates multiple prosurvival pathways, including MAPK and cell-cycle regulation in MEKi-resistant cells. Employing combination strategies to simultaneously target these pathways heightened growth inhibition in AML cells. Both genetic and pharmacologic inhibition of CCR2 sensitized AML cells to trametinib, suppressing proliferation while enhancing apoptosis. These findings underscore a new role for CCL2 in MEKi resistance, offering combination therapies as an avenue to circumvent this resistance. CONCLUSIONS Our study demonstrates a compelling rationale for translating CCL2/CCR2 axis inhibitors in combination with MEK pathway-targeting therapies, as a potent strategy for combating drug resistance in AML. This approach has the potential to enhance the efficacy of treatments to improve AML patient outcomes.
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MESH Headings
- Humans
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/pathology
- Receptors, CCR2/metabolism
- Receptors, CCR2/antagonists & inhibitors
- Receptors, CCR2/genetics
- Drug Resistance, Neoplasm/genetics
- Chemokine CCL2/metabolism
- Chemokine CCL2/genetics
- Protein Kinase Inhibitors/pharmacology
- Protein Kinase Inhibitors/therapeutic use
- Signal Transduction/drug effects
- Cell Line, Tumor
- Cell Proliferation/drug effects
- Animals
- Pyridones/pharmacology
- Pyridones/therapeutic use
- Mice
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Affiliation(s)
- Rucha V. Modak
- Division of Oncological Sciences, Oregon Health & Science University, Portland, Oregon
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, Oregon
- Department of Cell, Developmental, & Cancer Biology, Oregon Health & Science University, Portland, Oregon
| | - Katia G. de Oliveira Rebola
- Division of Oncological Sciences, Oregon Health & Science University, Portland, Oregon
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, Oregon
- Department of Cell, Developmental, & Cancer Biology, Oregon Health & Science University, Portland, Oregon
| | - John McClatchy
- Division of Oncological Sciences, Oregon Health & Science University, Portland, Oregon
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, Oregon
- Department of Cell, Developmental, & Cancer Biology, Oregon Health & Science University, Portland, Oregon
| | - Mona Mohammadhosseini
- Division of Oncological Sciences, Oregon Health & Science University, Portland, Oregon
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, Oregon
- Department of Cell, Developmental, & Cancer Biology, Oregon Health & Science University, Portland, Oregon
| | - Alisa Damnernsawad
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
- Department of Cell, Developmental, & Cancer Biology, Oregon Health & Science University, Portland, Oregon
- Department of Biology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Stephen E. Kurtz
- Division of Oncological Sciences, Oregon Health & Science University, Portland, Oregon
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
- Department of Cell, Developmental, & Cancer Biology, Oregon Health & Science University, Portland, Oregon
| | - Christopher A. Eide
- Division of Oncological Sciences, Oregon Health & Science University, Portland, Oregon
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
| | - Guanming Wu
- Division of Bioinformatics & Computational Biology, Oregon Health & Science University, Portland, Oregon
| | - Ted Laderas
- Division of Bioinformatics & Computational Biology, Oregon Health & Science University, Portland, Oregon
| | - Tamilla Nechiporuk
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
- Department of Cell, Developmental, & Cancer Biology, Oregon Health & Science University, Portland, Oregon
| | | | | | | | - Sara J.C. Gosline
- Pacific Northwest National Laboratory, Richland, Washington
- Department of Biomedical Engineering, School of Medicine, Oregon Health & Science University, Portland, Oregon
| | - Paul Piehowski
- Pacific Northwest National Laboratory, Richland, Washington
| | - Daniel Bottomly
- Division of Bioinformatics & Computational Biology, Oregon Health & Science University, Portland, Oregon
| | - Nicholas Short
- Department of Leukemia, MD Anderson Cancer Center, Houston, Texas
| | - Karin Rodland
- Pacific Northwest National Laboratory, Richland, Washington
| | - Shannon K. McWeeney
- Division of Bioinformatics & Computational Biology, Oregon Health & Science University, Portland, Oregon
| | - Jeffrey W. Tyner
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
- Department of Cell, Developmental, & Cancer Biology, Oregon Health & Science University, Portland, Oregon
| | - Anupriya Agarwal
- Division of Oncological Sciences, Oregon Health & Science University, Portland, Oregon
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, Oregon
- Department of Cell, Developmental, & Cancer Biology, Oregon Health & Science University, Portland, Oregon
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3
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Bhatia K, Sandhu V, Wong MH, Iyer P, Bhatt S. Therapeutic biomarkers in acute myeloid leukemia: functional and genomic approaches. Front Oncol 2024; 14:1275251. [PMID: 38410111 PMCID: PMC10894932 DOI: 10.3389/fonc.2024.1275251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 01/17/2024] [Indexed: 02/28/2024] Open
Abstract
Acute myeloid leukemia (AML) is clinically and genetically a heterogeneous disease characterized by clonal expansion of abnormal hematopoietic progenitors. Genomic approaches to precision medicine have been implemented to direct targeted therapy for subgroups of AML patients, for instance, IDH inhibitors for IDH1/2 mutated patients, and FLT3 inhibitors with FLT3 mutated patients. While next generation sequencing for genetic mutations has improved treatment outcomes, only a fraction of AML patients benefit due to the low prevalence of actionable targets. In recent years, the adoption of newer functional technologies for quantitative phenotypic analysis and patient-derived avatar models has strengthened the potential for generalized functional precision medicine approach. However, functional approach requires robust standardization for multiple variables such as functional parameters, time of drug exposure and drug concentration for making in vitro predictions. In this review, we first summarize genomic and functional therapeutic biomarkers adopted for AML therapy, followed by challenges associated with these approaches, and finally, the future strategies to enhance the implementation of precision medicine.
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Affiliation(s)
- Karanpreet Bhatia
- Department of Pharmacy, National University of Singapore, Singapore, Singapore
| | - Vedant Sandhu
- Department of Pharmacy, National University of Singapore, Singapore, Singapore
| | - Mei Hsuan Wong
- Department of Pharmacy, National University of Singapore, Singapore, Singapore
| | - Prasad Iyer
- Children's Blood and Cancer Centre, KK Women's and Children's Hospital, Singapore, Singapore
- Duke-National University of Singapore (NUS) Medical School, Singapore, Singapore
| | - Shruti Bhatt
- Department of Pharmacy, National University of Singapore, Singapore, Singapore
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4
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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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5
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Stephenson EH, Higgins JMG. Pharmacological approaches to understanding protein kinase signaling networks. Front Pharmacol 2023; 14:1310135. [PMID: 38164473 PMCID: PMC10757940 DOI: 10.3389/fphar.2023.1310135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 11/27/2023] [Indexed: 01/03/2024] Open
Abstract
Protein kinases play vital roles in controlling cell behavior, and an array of kinase inhibitors are used successfully for treatment of disease. Typical drug development pipelines involve biological studies to validate a protein kinase target, followed by the identification of small molecules that effectively inhibit this target in cells, animal models, and patients. However, it is clear that protein kinases operate within complex signaling networks. These networks increase the resilience of signaling pathways, which can render cells relatively insensitive to inhibition of a single kinase, and provide the potential for pathway rewiring, which can result in resistance to therapy. It is therefore vital to understand the properties of kinase signaling networks in health and disease so that we can design effective multi-targeted drugs or combinations of drugs. Here, we outline how pharmacological and chemo-genetic approaches can contribute to such knowledge, despite the known low selectivity of many kinase inhibitors. We discuss how detailed profiling of target engagement by kinase inhibitors can underpin these studies; how chemical probes can be used to uncover kinase-substrate relationships, and how these tools can be used to gain insight into the configuration and function of kinase signaling networks.
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Affiliation(s)
| | - Jonathan M. G. Higgins
- Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle uponTyne, United Kingdom
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6
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Ayuda-Durán P, Hermansen JU, Giliberto M, Yin Y, Hanes R, Gordon S, Kuusanmäki H, Brodersen AM, Andersen AN, Taskén K, Wennerberg K, Enserink JM, Skånland SS. Standardized assays to monitor drug sensitivity in hematologic cancers. Cell Death Discov 2023; 9:435. [PMID: 38040674 PMCID: PMC10692209 DOI: 10.1038/s41420-023-01722-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 10/21/2023] [Accepted: 11/13/2023] [Indexed: 12/03/2023] Open
Abstract
The principle of drug sensitivity testing is to expose cancer cells to a library of different drugs and measure its effects on cell viability. Recent technological advances, continuous approval of targeted therapies, and improved cell culture protocols have enhanced the precision and clinical relevance of such screens. Indeed, drug sensitivity testing has proven diagnostically valuable for patients with advanced hematologic cancers. However, different cell types behave differently in culture and therefore require optimized drug screening protocols to ensure that their ex vivo drug sensitivity accurately reflects in vivo drug responses. For example, primary chronic lymphocytic leukemia (CLL) and multiple myeloma (MM) cells require unique microenvironmental stimuli to survive in culture, while this is less the case for acute myeloid leukemia (AML) cells. Here, we present our optimized and validated protocols for culturing and drug screening of primary cells from AML, CLL, and MM patients, and a generic protocol for cell line models. We also discuss drug library designs, reproducibility, and quality controls. We envision that these protocols may serve as community guidelines for the use and interpretation of assays to monitor drug sensitivity in hematologic cancers and thus contribute to standardization. The read-outs may provide insight into tumor biology, identify or confirm treatment resistance and sensitivity in real time, and ultimately guide clinical decision-making.
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Affiliation(s)
- Pilar Ayuda-Durán
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Johanne U Hermansen
- 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
| | - Mariaserena Giliberto
- 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
| | - Yanping Yin
- 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
- Department of Haematology, Oslo University Hospital, Oslo, Norway
| | - Robert Hanes
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Section for Biochemistry and Molecular Biology, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - Sandra Gordon
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - Heikki Kuusanmäki
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Andrea M Brodersen
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Section for Biochemistry and Molecular Biology, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - Aram N Andersen
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Section for Biochemistry and Molecular Biology, Faculty of Mathematics and Natural Sciences, 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
| | - Krister Wennerberg
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - Jorrit M Enserink
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Section for Biochemistry and Molecular Biology, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, 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.
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7
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Herbst SA, Kim V, Roider T, Schitter EC, Bruch PM, Liebers N, Kolb C, Knoll M, Lu J, Dreger P, Müller-Tidow C, Zenz T, Huber W, Dietrich S. Comparing the value of mono- vs coculture for high-throughput compound screening in hematological malignancies. Blood Adv 2023; 7:5925-5936. [PMID: 37352275 PMCID: PMC10558604 DOI: 10.1182/bloodadvances.2022009652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 05/19/2023] [Accepted: 06/07/2023] [Indexed: 06/25/2023] Open
Abstract
Large-scale compound screens are a powerful model system for understanding variability of treatment response and discovering druggable tumor vulnerabilities of hematological malignancies. However, as mostly performed in a monoculture of tumor cells, these assays disregard modulatory effects of the in vivo microenvironment. It is an open question whether and to what extent coculture with bone marrow stromal cells could improve the biological relevance of drug testing assays over monoculture. Here, we established a high-throughput platform to measure ex vivo sensitivity of 108 primary blood cancer samples to 50 drugs in monoculture and coculture with bone marrow stromal cells. Stromal coculture conferred resistance to 52% of compounds in chronic lymphocytic leukemia (CLL) and 36% of compounds in acute myeloid leukemia (AML), including chemotherapeutics, B-cell receptor inhibitors, proteasome inhibitors, and Bromodomain and extraterminal domain inhibitors. Only the JAK inhibitors ruxolitinib and tofacitinib exhibited increased efficacy in AML and CLL stromal coculture. We further confirmed the importance of JAK-STAT signaling for stroma-mediated resistance by showing that stromal cells induce phosphorylation of STAT3 in CLL cells. We genetically characterized the 108 cancer samples and found that drug-gene associations strongly correlated between monoculture and coculture. However, effect sizes were lower in coculture, with more drug-gene associations detected in monoculture than in coculture. Our results justify a 2-step strategy for drug perturbation testing, with large-scale screening performed in monoculture, followed by focused evaluation of potential stroma-mediated resistances in coculture.
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Affiliation(s)
- Sophie A. Herbst
- Department of Medicine V, Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Molecular Medicine Partnership Unit, Heidelberg, Germany
- Department of Translational Medical Oncology, National Center for Tumor Diseases Heidelberg, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
| | - Vladislav Kim
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Molecular Medicine Partnership Unit, Heidelberg, Germany
- Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
| | - Tobias Roider
- Department of Medicine V, Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Molecular Medicine Partnership Unit, Heidelberg, Germany
| | - Eva C. Schitter
- Department of Medicine V, Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany
| | - Peter-Martin Bruch
- Department of Medicine V, Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Molecular Medicine Partnership Unit, Heidelberg, Germany
- Department of Hematology and Oncology, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Nora Liebers
- Department of Medicine V, Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Molecular Medicine Partnership Unit, Heidelberg, Germany
- Department of Translational Medical Oncology, National Center for Tumor Diseases Heidelberg, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Carolin Kolb
- Department of Medicine V, Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany
| | - Mareike Knoll
- Department of Medicine V, Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany
| | - Junyan Lu
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Molecular Medicine Partnership Unit, Heidelberg, Germany
| | - Peter Dreger
- Department of Medicine V, Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany
| | - Carsten Müller-Tidow
- Department of Medicine V, Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Molecular Medicine Partnership Unit, Heidelberg, Germany
| | - Thorsten Zenz
- Department of Medical Oncology and Hematology, University Hospital Zürich, Zürich, Switzerland
| | - Wolfgang Huber
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Molecular Medicine Partnership Unit, Heidelberg, Germany
| | - Sascha Dietrich
- Department of Medicine V, Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Molecular Medicine Partnership Unit, Heidelberg, Germany
- Department of Hematology and Oncology, University Hospital Düsseldorf, Düsseldorf, Germany
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8
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Chien W, Tyner JW, Gery S, Zheng Y, Li LY, Gopinatha Pillai MS, Nam C, Bhowmick NA, Lin DC, Koeffler HP. Treatment for ovarian clear cell carcinoma with combined inhibition of WEE1 and ATR. J Ovarian Res 2023; 16:80. [PMID: 37087441 PMCID: PMC10122390 DOI: 10.1186/s13048-023-01160-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 04/10/2023] [Indexed: 04/24/2023] Open
Abstract
BACKGROUND Standard platinum-based therapy for ovarian cancer is inefficient against ovarian clear cell carcinoma (OCCC). OCCC is a distinct subtype of epithelial ovarian cancer. OCCC constitutes 25% of ovarian cancers in East Asia (Japan, Korea, China, Singapore) and 6-10% in Europe and North America. The cancer is characterized by frequent inactivation of ARID1A and 10% of cases of endometriosis progression to OCCC. The aim of this study was to identify drugs that are either FDA-approved or in clinical trials for the treatment of OCCC. RESULTS High throughput screening of 166 compounds that are either FDA-approved, in clinical trials or are in pre-clinical studies identified several cytotoxic compounds against OCCC. ARID1A knockdown cells were more sensitive to inhibitors of either mTOR (PP242), dual mTOR/PI3K (GDC0941), ATR (AZD6738) or MDM2 (RG7388) compared to control cells. Also, compounds targeting BH3 domain (AZD4320) and SRC (AZD0530) displayed preferential cytotoxicity against ARID1A mutant cell lines. In addition, WEE1 inhibitor (AZD1775) showed broad cytotoxicity toward OCCC cell lines, irrespective of ARID1A status. CONCLUSIONS In a selection of 166 compounds we showed that inhibitors of ATR and WEE1 were cytotoxic against a panel of OCCC cell lines. These two drugs are already in other clinical trials, making them ideal candidates for treatment of OCCC.
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Affiliation(s)
- Wenwen Chien
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA, 90048, USA.
| | - Jeffrey W Tyner
- Knight Cancer Institute, Oregon Health & Science University, Oregon Health and Science University, 2720 S.W. Moody Avenue, Portland, OR, 97201, USA
| | - Sigal Gery
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA, 90048, USA
| | - Yueyuan Zheng
- Clinical Big Data Research Center, Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, 518107, P. R. China
| | - Li-Yan Li
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, Guandong Province, P. R. China
| | - Mohan Shankar Gopinatha Pillai
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA, 90048, USA
| | - Chehyun Nam
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Neil A Bhowmick
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA, 90048, USA
| | - De-Chen Lin
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA, 90089, USA
| | - H Phillip Koeffler
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA, 90048, USA
- Department of Hematology-Oncology, National University Cancer Institute of Singapore, National University Hospital, Singapore, 119074, Singapore
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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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Therapeutic Targeting of MERTK and BCL-2 in T-Cell and Early T-Precursor Acute Lymphoblastic Leukemia. Cancers (Basel) 2022; 14:cancers14246142. [PMID: 36551626 PMCID: PMC9776749 DOI: 10.3390/cancers14246142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 12/05/2022] [Accepted: 12/12/2022] [Indexed: 12/15/2022] Open
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) accounts for 15% of childhood ALL. The early T-precursor (ETP-ALL) subset is characterized by an immature T-cell phenotype, chemoresistance, and high rates of induction failure. MERTK receptor tyrosine kinase is ectopically expressed in half of T-ALLs, particularly those with an immature T-cell phenotype, suggesting a role in ETP-ALL. The anti-apoptotic protein B-cell lymphoma-2 (BCL-2) is essential for ETP-ALL cell survival. Here, we show that MERTK and BCL-2 mRNA and protein are preferentially expressed in ETP-ALL patient samples. The dual MERTK/FLT3 inhibitor MRX-2843 decreased MERTK activation and downstream signaling, inhibited cell expansion, and induced cell death in ETP-ALL cell lines. Further, 54% (21/39) of primary T-ALL patient samples were sensitive to MERTK inhibition. Treatment with MRX-2843 significantly reduced leukemia burden and prolonged survival in cell-line-derived T-ALL and ETP-ALL xenograft models. In a patient-derived ETP-ALL xenograft model, treatment with MRX-2843 markedly reduced peripheral blood leukemia and spleen weight compared to vehicle-treated mice and prolonged survival. MRX-2843 also synergized with venetoclax to provide enhanced anti-leukemia activity in ETP-ALL cell cultures, with a dose ratio of 1:20 MRX-2843:venetoclax providing optimal synergy. These data demonstrate the therapeutic potential of MRX-2843 in patients with T-ALL and provide rationale for clinical development. MRX-2843 monotherapy is currently being tested in patients with relapsed leukemia (NCT04872478). Further, our data indicate that combined MERTK and BCL-2 inhibition may be particularly effective for treatment of ETP-ALL.
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11
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Comprehensive molecular characterization of a rare case of Philadelphia chromosome-positive acute myeloid leukemia. Cold Spring Harb Mol Case Stud 2022; 8:mcs.a006218. [PMID: 36307214 PMCID: PMC9632359 DOI: 10.1101/mcs.a006218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 09/23/2022] [Indexed: 01/25/2023] Open
Abstract
The Philadelphia chromosome (Ph) resulting from the t(9;22) translocation generates the oncogenic BCR::ABL1 fusion protein that is most commonly associated with chronic myeloid leukemia (CML) and Ph-positive (Ph+) acute lymphoblastic leukemia (ALL). There are also rare instances of patients (≤1%) with newly diagnosed acute myeloid leukemia (AML) that harbor this translocation (Paietta et al., Leukemia 12: 1881 [1998]; Keung et al., Leuk Res 28: 579 [2004]; Soupir et al., Am J Clin Pathol 127: 642 [2007]). AML with BCR::ABL has only recently been provisionally classified by the World Health Organization as a diagnostically distinct subtype of AML. Discernment from the extremely close differential diagnosis of myeloid blast crisis CML is challenging, largely relying on medical history rather than clinical characteristics (Arber et al., Blood 127: 2391 [2016]). To gain insight into the genomic features underlying the evolution of AML with BCR::ABL, we identified a patient presenting with a high-risk myelodysplastic syndrome that acquired a BCR::ABL alteration after a peripheral blood stem cell transplant. Serial samples were collected and analyzed using whole-exome sequencing, RNA-seq, and ex vivo functional drug screens. Persistent subclones were identified, both at diagnosis and at relapse, including an SF3B1p.Lys700Glu mutation that later cooccurred with an NRASp.Gly12Cys mutation. Functional ex vivo drug screening performed on primary patient cells suggested that combination therapies of ABL1 with RAS or PI3K pathway inhibitors could have augmented the patient's response throughout the course of disease. Together, our findings argue for the importance of genomic profiling and the potential value of ABL1 inhibitor-inclusive combination treatment strategies in patients with this rare disease.
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12
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Carratt SA, Kong GL, Curtiss BM, Schonrock Z, Maloney L, Maniaci BN, Blaylock HZ, Baris A, Druker BJ, Braun TP, Maxson JE. Mutated SETBP1 activates transcription of Myc programs to accelerate CSF3R-driven myeloproliferative neoplasms. Blood 2022; 140:644-658. [PMID: 35482940 PMCID: PMC9373012 DOI: 10.1182/blood.2021014777] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 04/15/2022] [Indexed: 11/20/2022] Open
Abstract
Colony stimulating factor 3 receptor (CSF3R) mutations lead to JAK pathway activation and are the molecular hallmark of chronic neutrophilic leukemia (CNL). Approximately half of patients with CNL also have mutations in SET binding protein 1 (SETBP1). In this study, we developed models of SETBP1-mutated leukemia to understand the role that SETBP1 plays in CNL. SETBP1 mutations promote self-renewal of CSF3R-mutated hematopoietic progenitors in vitro and prevent cells from undergoing terminal differentiation. In vivo, SETBP1 mutations accelerate leukemia progression, leading to the rapid development of hepatosplenomegaly and granulocytosis. Through transcriptomic and epigenomic profiling, we found that SETBP1 enhances progenitor-associated programs, most strongly upregulating Myc and Myc target genes. This upregulation of Myc can be reversed by LSD1 inhibitors. In summary, we found that SETBP1 mutations promote aggressive hematopoietic cell expansion when expressed with mutated CSF3R through the upregulation of Myc-associated gene expression programs.
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Affiliation(s)
- Sarah A Carratt
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
| | - Garth L Kong
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
| | - Brittany M Curtiss
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
| | - Zachary Schonrock
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
| | - Lauren Maloney
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
| | - Breanna N Maniaci
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
| | - Hunter Z Blaylock
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
| | - Adrian Baris
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
| | - Brian J Druker
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
| | - Theodore P Braun
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
| | - Julia E Maxson
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
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13
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Dozzo A, Galvin A, Shin JW, Scalia S, O'Driscoll CM, Ryan KB. Modelling acute myeloid leukemia (AML): What's new? A transition from the classical to the modern. Drug Deliv Transl Res 2022:10.1007/s13346-022-01189-4. [PMID: 35930221 DOI: 10.1007/s13346-022-01189-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2022] [Indexed: 11/24/2022]
Abstract
Acute myeloid leukemia (AML) is a heterogeneous malignancy affecting myeloid cells in the bone marrow (BM) but can spread giving rise to impaired hematopoiesis. AML incidence increases with age and is associated with poor prognostic outcomes. There has been a disconnect between the success of novel drug compounds observed in preclinical studies of hematological malignancy and less than exceptional therapeutic responses in clinical trials. This review aims to provide a state-of-the-art overview on the different preclinical models of AML available to expand insights into disease pathology and as preclinical screening tools. Deciphering the complex physiological and pathological processes and developing predictive preclinical models are key to understanding disease progression and fundamental in the development and testing of new effective drug treatments. Standard scaffold-free suspension models fail to recapitulate the complex environment where AML occurs. To this end, we review advances in scaffold/matrix-based 3D models and outline the most recent advances in on-chip technology. We also provide an overview of clinically relevant animal models and review the expanding use of patient-derived samples, which offer the prospect to create more "patient specific" screening tools either in the guise of 3D matrix models, microphysiological "organ-on-chip" tools or xenograft models and discuss representative examples.
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Affiliation(s)
| | - Aoife Galvin
- School of Pharmacy, University College Cork, Cork, Ireland
| | - Jae-Won Shin
- Department of Pharmacology and Regenerative Medicine, University of Illinois at Chicago College of Medicine, 909 S. Wolcott Ave, Chicago, IL, 5091 COMRB, USA
| | - Santo Scalia
- Università degli Studi di Ferrara, Via Luigi Borsari 46, 44121, Ferrara, Italy
| | - Caitriona M O'Driscoll
- School of Pharmacy, University College Cork, Cork, Ireland.,SSPC Centre for Pharmaceutical Research, School of Pharmacy, University College Cork, Cork, Ireland
| | - Katie B Ryan
- School of Pharmacy, University College Cork, Cork, Ireland. .,SSPC Centre for Pharmaceutical Research, School of Pharmacy, University College Cork, Cork, Ireland.
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14
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Dal Bello R, Pasanisi J, Joudinaud R, Duchmann M, Pardieu B, Ayaka P, Di Feo G, Sodaro G, Chauvel C, Kim R, Vasseur L, Chat L, Ling F, Pacchiardi K, Vaganay C, Berrou J, Benaksas C, Boissel N, Braun T, Preudhomme C, Dombret H, Raffoux E, Fenouille N, Clappier E, Adès L, Puissant A, Itzykson R. A multiparametric niche-like drug screening platform in acute myeloid leukemia. Blood Cancer J 2022; 12:95. [PMID: 35750691 PMCID: PMC9232632 DOI: 10.1038/s41408-022-00689-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 05/13/2022] [Accepted: 06/07/2022] [Indexed: 02/06/2023] Open
Abstract
Functional precision medicine in AML often relies on short-term in vitro drug sensitivity screening (DSS) of primary patient cells in standard culture conditions. We designed a niche-like DSS assay combining physiologic hypoxia (O2 3%) and mesenchymal stromal cell (MSC) co-culture with multiparameter flow cytometry to enumerate lymphocytes and differentiating (CD11/CD14/CD15+) or leukemic stem cell (LSC)-enriched (GPR56+) cells within the leukemic bulk. After functional validation of GPR56 expression as a surrogate for LSC enrichment, the assay identified three patterns of response, including cytotoxicity on blasts sparing LSCs, induction of differentiation, and selective impairment of LSCs. We refined our niche-like culture by including plasma-like amino-acid and cytokine concentrations identified by targeted metabolomics and proteomics of primary AML bone marrow plasma samples. Systematic interrogation revealed distinct contributions of each niche-like component to leukemic outgrowth and drug response. Short-term niche-like culture preserved clonal architecture and transcriptional states of primary leukemic cells. In a cohort of 45 AML samples enriched for NPM1c AML, the niche-like multiparametric assay could predict morphologically (p = 0.02) and molecular (NPM1c MRD, p = 0.04) response to anthracycline-cytarabine induction chemotherapy. In this cohort, a 23-drug screen nominated ruxolitinib as a sensitizer to anthracycline-cytarabine. This finding was validated in an NPM1c PDX model.
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Affiliation(s)
- Reinaldo Dal Bello
- Université Paris Cité, Génomes, biologie cellulaire et thérapeutique U944, INSERM, CNRS, F-75010, Paris, France.,Service Hématologie Adultes, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, F-75010, Paris, France
| | - Justine Pasanisi
- Université Paris Cité, Génomes, biologie cellulaire et thérapeutique U944, INSERM, CNRS, F-75010, Paris, France
| | - Romane Joudinaud
- Univ. Lille, CNRS, Inserm, CHU Lille, IRCL, UMR9020 - UMR1277 - Canther - Cancer Heterogeneity, Plasticity and Resistance to Therapies, F-59000, Lille, France
| | - Matthieu Duchmann
- Université Paris Cité, Génomes, biologie cellulaire et thérapeutique U944, INSERM, CNRS, F-75010, Paris, France
| | - Bryann Pardieu
- Université Paris Cité, Génomes, biologie cellulaire et thérapeutique U944, INSERM, CNRS, F-75010, Paris, France
| | - Paolo Ayaka
- Université Paris Cité, Génomes, biologie cellulaire et thérapeutique U944, INSERM, CNRS, F-75010, Paris, France
| | - Giuseppe Di Feo
- Université Paris Cité, Génomes, biologie cellulaire et thérapeutique U944, INSERM, CNRS, F-75010, Paris, France
| | - Gaetano Sodaro
- Université Paris Cité, Génomes, biologie cellulaire et thérapeutique U944, INSERM, CNRS, F-75010, Paris, France
| | - Clémentine Chauvel
- Université Paris Cité, Génomes, biologie cellulaire et thérapeutique U944, INSERM, CNRS, F-75010, Paris, France.,Laboratoire d'Hématologie, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, F-75010, Paris, France
| | - Rathana Kim
- Université Paris Cité, Génomes, biologie cellulaire et thérapeutique U944, INSERM, CNRS, F-75010, Paris, France.,Laboratoire d'Hématologie, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, F-75010, Paris, France
| | - Loic Vasseur
- Université Paris Cité, Génomes, biologie cellulaire et thérapeutique U944, INSERM, CNRS, F-75010, Paris, France
| | - Laureen Chat
- Université Paris Cité, Génomes, biologie cellulaire et thérapeutique U944, INSERM, CNRS, F-75010, Paris, France
| | - Frank Ling
- Université Paris Cité, Génomes, biologie cellulaire et thérapeutique U944, INSERM, CNRS, F-75010, Paris, France
| | - Kim Pacchiardi
- Université Paris Cité, Génomes, biologie cellulaire et thérapeutique U944, INSERM, CNRS, F-75010, Paris, France.,Laboratoire d'Hématologie, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, F-75010, Paris, France
| | - Camille Vaganay
- Université Paris Cité, Génomes, biologie cellulaire et thérapeutique U944, INSERM, CNRS, F-75010, Paris, France
| | - Jeannig Berrou
- Université Paris Cité, EA 3518, IRSL, Hôpital Saint-Louis, F-75010, Paris, France
| | - Chaima Benaksas
- Université Paris Cité, Génomes, biologie cellulaire et thérapeutique U944, INSERM, CNRS, F-75010, Paris, France
| | - Nicolas Boissel
- Service Hématologie Adolescents Jeunes Adultes, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, F-75010, Paris, France
| | - Thorsten Braun
- Université Paris Cité, EA 3518, IRSL, Hôpital Saint-Louis, F-75010, Paris, France.,Service d'Hématologie clinique, Hôpital Avicenne, Assistance Publique-Hôpitaux de Paris, Bobigny, France
| | - Claude Preudhomme
- Univ. Lille, CNRS, Inserm, CHU Lille, IRCL, UMR9020 - UMR1277 - Canther - Cancer Heterogeneity, Plasticity and Resistance to Therapies, F-59000, Lille, France
| | - Hervé Dombret
- Service Hématologie Adultes, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, F-75010, Paris, France.,Université Paris Cité, EA 3518, IRSL, Hôpital Saint-Louis, F-75010, Paris, France
| | - Emmanuel Raffoux
- Service Hématologie Adultes, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, F-75010, Paris, France
| | - Nina Fenouille
- Université Paris Cité, Génomes, biologie cellulaire et thérapeutique U944, INSERM, CNRS, F-75010, Paris, France
| | - Emmanuelle Clappier
- Université Paris Cité, Génomes, biologie cellulaire et thérapeutique U944, INSERM, CNRS, F-75010, Paris, France.,Laboratoire d'Hématologie, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, F-75010, Paris, France
| | - Lionel Adès
- Service Hématologie Seniors, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, F-75010, Paris, France
| | - Alexandre Puissant
- Université Paris Cité, Génomes, biologie cellulaire et thérapeutique U944, INSERM, CNRS, F-75010, Paris, France
| | - Raphael Itzykson
- Université Paris Cité, Génomes, biologie cellulaire et thérapeutique U944, INSERM, CNRS, F-75010, Paris, France. .,Service Hématologie Adultes, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, F-75010, Paris, France.
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15
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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: 59] [Impact Index Per Article: 29.5] [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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16
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Letai A. Functional Precision Medicine: Putting Drugs on Patient Cancer Cells and Seeing What Happens. Cancer Discov 2022; 12:290-292. [PMID: 35140175 PMCID: PMC8852353 DOI: 10.1158/2159-8290.cd-21-1498] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
For too long, assays exposing patient tumor cells to drugs to identify active therapies have been dismissed as ineffective. In this issue of Cancer Discovery, two groups independently demonstrate clinical utility of such functional precision medicine assays in hematologic malignancies.See related article by Kornauth et al., p. 372.See related article by Malani et al., p. 388.
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Affiliation(s)
- Anthony Letai
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.
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17
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Genomic Abnormalities as Biomarkers and Therapeutic Targets in Acute Myeloid Leukemia. Cancers (Basel) 2021; 13:cancers13205055. [PMID: 34680203 PMCID: PMC8533805 DOI: 10.3390/cancers13205055] [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: 09/11/2021] [Revised: 10/01/2021] [Accepted: 10/08/2021] [Indexed: 11/17/2022] Open
Abstract
Simple Summary AML is a heterogenous malignancy with a variety of underlying genomic abnormalities. Some of the genetic aberrations in AML have led to the development of specific inhibitors which were approved by the Food and Drug Administration (FDA) and are currently used to treat eligible patients. In this review, we describe five gene mutations for which approved inhibitors have been developed, the response of AML patients to these inhibitors, and the known mechanism(s) of resistance. This review also highlights the significance of developing function-based screens for target discovery in the era of personalized medicine. Abstract Acute myeloid leukemia (AML) is a highly heterogeneous malignancy characterized by the clonal expansion of myeloid stem and progenitor cells in the bone marrow, peripheral blood, and other tissues. AML results from the acquisition of gene mutations or chromosomal abnormalities that induce proliferation or block differentiation of hematopoietic progenitors. A combination of cytogenetic profiling and gene mutation analyses are essential for the proper diagnosis, classification, prognosis, and treatment of AML. In the present review, we provide a summary of genomic abnormalities in AML that have emerged as both markers of disease and therapeutic targets. We discuss the abnormalities of RARA, FLT3, BCL2, IDH1, and IDH2, their significance as therapeutic targets in AML, and how various mechanisms cause resistance to the currently FDA-approved inhibitors. We also discuss the limitations of current genomic approaches for producing a comprehensive picture of the activated signaling pathways at diagnosis or at relapse in AML patients, and how innovative technologies combining genomic and functional methods will improve the discovery of novel therapeutic targets in AML. The ultimate goal is to optimize a personalized medicine approach for AML patients and possibly those with other types of cancers.
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18
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Nykänen N, Mäkelä R, Arjonen A, Härmä V, Lewandowski L, Snowden E, Blaesius R, Jantunen I, Kuopio T, Kononen J, Rantala JK. Ex Vivo Drug Screening Informed Targeted Therapy for Metastatic Parotid Squamous Cell Carcinoma. Front Oncol 2021; 11:735820. [PMID: 34604070 PMCID: PMC8481915 DOI: 10.3389/fonc.2021.735820] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 08/23/2021] [Indexed: 11/13/2022] Open
Abstract
The purpose of ex vivo drug screening in the context of precision oncology is to serve as a functional diagnostic method for therapy efficacy modeling directly on patient-derived tumor cells. Here, we report a case study using integrated multiomics ex vivo drug screening approach to assess therapy efficacy in a rare metastatic squamous cell carcinoma of the parotid gland. Tumor cells isolated from lymph node metastasis and distal subcutaneous metastasis were used for imaging-based single-cell resolution drug screening and reverse-phase protein array-based drug screening assays to inform the treatment strategy after standard therapeutic options had been exhausted. The drug targets discovered on the basis of the ex vivo measured drug efficacy were validated with histopathology, genomic profiling, and in vitro cell biology methods, and targeted treatments with durable clinical responses were achieved. These results demonstrate the use of serial ex vivo drug screening to inform adjuvant therapy options prior to and during treatment and highlight HER2 as a potential therapy target also in metastatic squamous cell carcinoma of the salivary glands.
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Affiliation(s)
| | | | | | - Ville Härmä
- Misvik Biology Oy, Turku, Finland.,Department of Oncology and Metabolism, University of Sheffield, Sheffield, United Kingdom
| | | | - Eileen Snowden
- Genomic Sciences, BD Technologies, Research Triangle Park, Durham, NC, United States
| | - Rainer Blaesius
- Genomic Sciences, BD Technologies, Research Triangle Park, Durham, NC, United States
| | - Ismo Jantunen
- Central Finland Health Care District, Jyväskylä, Finland
| | - Teijo Kuopio
- Central Finland Health Care District, Jyväskylä, Finland.,Department of Biological and Environmental Science, Jyväskylä, Finland
| | | | - Juha K Rantala
- Misvik Biology Oy, Turku, Finland.,Department of Oncology and Metabolism, University of Sheffield, Sheffield, United Kingdom
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19
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A novel activating JAK1 mutation in chronic eosinophilic leukemia. Blood Adv 2021; 5:3581-3586. [PMID: 34496019 DOI: 10.1182/bloodadvances.2021004237] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 06/02/2021] [Indexed: 01/08/2023] Open
Abstract
Hypereosinophilia (HE) has been defined as persistent eosinophilia >1.5 × 109/L; it is broadly divided into primary HE (clonal or neoplastic; HEN), secondary/reactive HE (HER), or HE of undetermined significance (HEUS) when no cause is identified. The use of myeloid next-generation sequencing (NGS) panels has led to the detection of several mutations in patients previously diagnosed with HEUS, reassigning some patients to the category of HEN, specifically the World Health Organization category of chronic eosinophilic leukemia, not otherwise specified (CEL, NOS). Here, we describe a novel somatic JAK1 pseudokinase domain mutation (R629_S632delinsSA) in a patient with HE that had initially been characterized as a variant of uncertain significance. We performed functional studies that demonstrated that this mutation results in growth factor independence of Ba/F3 cells in vitro and activation of the JAK-STAT pathway. These effects were abrogated by the JAK1/JAK2 inhibitor ruxolitinib. R629_S632delinsSA is the first known somatic mutation in JAK1 linked to a clonal eosinophilic neoplasm, and highlights the importance of the JAK-STAT pathway in eosinophil survival.
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20
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Talwelkar SS, Mäyränpää MI, Søraas L, Potdar S, Bao J, Hemmes A, Linnavirta N, Lømo J, Räsänen J, Knuuttila A, Wennerberg K, Verschuren EW. Functional diagnostics using fresh uncultured lung tumor cells to guide personalized treatments. Cell Rep Med 2021; 2:100373. [PMID: 34467250 PMCID: PMC8385325 DOI: 10.1016/j.xcrm.2021.100373] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 04/20/2021] [Accepted: 07/20/2021] [Indexed: 12/25/2022]
Abstract
Functional profiling of a cancer patient's tumor cells holds potential to tailor personalized cancer treatment. Here, we report the utility of fresh uncultured tumor-derived EpCAM+ epithelial cells (FUTCs) for ex vivo drug-response interrogation. Analysis of murine Kras mutant FUTCs demonstrates pharmacological and adaptive signaling profiles comparable to subtype-matched cultured cells. By applying FUTC profiling on non-small-cell lung cancer patient samples, we report robust drug-response data in 19 of 20 cases, with cells exhibiting targeted drug sensitivities corresponding to their oncogenic drivers. In one of these cases, an EGFR mutant lung adenocarcinoma patient refractory to osimertinib, FUTC profiling is used to guide compassionate treatment. FUTC profiling identifies selective sensitivity to disulfiram and the combination of carboplatin plus etoposide, and the patient receives substantial clinical benefit from treatment with these agents. We conclude that FUTC profiling provides a robust, rapid, and actionable assessment of personalized cancer treatment options.
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Affiliation(s)
- Sarang S. Talwelkar
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki 00014, Finland
| | - Mikko I. Mäyränpää
- HUSLAB, Division of Pathology, Helsinki University Hospital and University of Helsinki, Helsinki 00029, Finland
- Department of Pathology, University of Helsinki, Helsinki 00014, Finland
| | | | - Swapnil Potdar
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki 00014, Finland
| | - Jie Bao
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki 00014, Finland
| | - Annabrita Hemmes
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki 00014, Finland
| | - Nora Linnavirta
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki 00014, Finland
| | - Jon Lømo
- Department of Pathology, Oslo University Hospital, Oslo, Norway
| | - Jari Räsänen
- Department of Thoracic Surgery, Heart and Lung Center, Helsinki University Hospital, Helsinki, Finland
| | - Aija Knuuttila
- Department of Pulmonary Medicine, Heart and Lung Center, and Cancer Center, Helsinki University Hospital, Helsinki, Finland
| | - Krister Wennerberg
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki 00014, Finland
- BRIC-Biotech Research & Innovation Centre and Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, 2200 Copenhagen, Denmark
| | - Emmy W. Verschuren
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki 00014, Finland
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21
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Antileukemic efficacy of a potent artemisinin combined with sorafenib and venetoclax. Blood Adv 2021; 5:711-724. [PMID: 33560385 DOI: 10.1182/bloodadvances.2020003429] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 12/28/2020] [Indexed: 12/21/2022] Open
Abstract
Artemisinins are active against human leukemia cell lines and have low clinical toxicity in worldwide use as antimalarials. Because multiagent combination regimens are necessary to cure fully evolved leukemias, we sought to leverage our previous finding that artemisinin analogs synergize with kinase inhibitors, including sorafenib (SOR), by identifying additional synergistic antileukemic drugs with low toxicity. Screening of a targeted antineoplastic drug library revealed that B-cell lymphoma 2 (BCL2) inhibitors synergize with artemisinins, and validation assays confirmed that the selective BCL2 inhibitor, venetoclax (VEN), synergized with artemisinin analogs to inhibit growth and induce apoptotic cell death of multiple acute leukemia cell lines in vitro. An oral 3-drug "SAV" regimen (SOR plus the potent artemisinin-derived trioxane diphenylphosphate 838 dimeric analog [ART838] plus VEN) killed leukemia cell lines and primary cells in vitro. Leukemia cells cultured in ART838 had decreased induced myeloid leukemia cell differentiation protein (MCL1) levels and increased levels of DNA damage-inducible transcript 3 (DDIT3; GADD153) messenger RNA and its encoded CCATT/enhancer-binding protein homologous protein (CHOP), a key component of the integrated stress response. Thus, synergy of the SAV combination may involve combined targeting of MCL1 and BCL2 via discrete, tolerable mechanisms, and cellular levels of MCL1 and DDIT3/CHOP may serve as biomarkers for action of artemisinins and SAV. Finally, SAV treatment was tolerable and resulted in deep responses with extended survival in 2 acute myeloid leukemia (AML) cell line xenograft models, both harboring a mixed lineage leukemia gene rearrangement and an FMS-like receptor tyrosine kinase-3 internal tandem duplication, and inhibited growth in 2 AML primagraft models.
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22
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Memon D, Gill MB, Papachristou EK, Ochoa D, D'Santos CS, Miller ML, Beltrao P. Copy number aberrations drive kinase rewiring, leading to genetic vulnerabilities in cancer. Cell Rep 2021; 35:109155. [PMID: 34010657 PMCID: PMC8149807 DOI: 10.1016/j.celrep.2021.109155] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 03/02/2021] [Accepted: 04/28/2021] [Indexed: 11/20/2022] Open
Abstract
Somatic DNA copy number variations (CNVs) are prevalent in cancer and can drive cancer progression, albeit with often uncharacterized roles in altering cell signaling states. Here, we integrate genomic and proteomic data for 5,598 tumor samples to identify CNVs leading to aberrant signal transduction. The resulting associations recapitulate known kinase-substrate relationships, and further network analysis prioritizes likely causal genes. Of the 303 significant associations we identify from the pan-tumor analysis, 43% are replicated in cancer cell lines, including 44 robust gene-phosphosite associations identified across multiple tumor types. Several predicted regulators of hippo signaling are experimentally validated. Using RNAi, CRISPR, and drug screening data, we find evidence of kinase addiction in cancer cell lines, identifying inhibitors for targeting of kinase-dependent cell lines. We propose copy number status of genes as a useful predictor of differential impact of kinase inhibition, a strategy that may be of use in the future for anticancer therapies.
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Affiliation(s)
- Danish Memon
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK; Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK
| | - Michael B Gill
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK
| | - Evangelia K Papachristou
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK
| | - David Ochoa
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Clive S D'Santos
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK
| | - Martin L Miller
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK.
| | - Pedro Beltrao
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
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23
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Preferential Activity of Petiveria alliacea Extract on Primary Myeloid Leukemic Blast. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2021; 2020:4736206. [PMID: 33488744 PMCID: PMC7787761 DOI: 10.1155/2020/4736206] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 10/14/2020] [Accepted: 11/15/2020] [Indexed: 12/18/2022]
Abstract
The need for new therapeutic approaches to improve the response in acute leukemia (AL), either by directing therapy or with new therapeutic alternatives, has been a research and clinical interest topic. We evaluated whether blasts from AL patients were sensitive ex vivo to the induction chemotherapy and whether the extracts of Petiveria alliacea (Anamu SC) and Caesalpinia spinosa (P2Et) modulated the sensitivity of leukemic cells to death. Bone marrow samples were taken from 26 patients with de novo AL and 6 in relapse, and the cytotoxicity of the extracts alone or in combination with the chemotherapeutic was evaluated by XTT. Patients were classified as good (GR) and bad responders (BR) according to the ex vivo test. 70.5% of the GR patients to the ex vivo test achieved postinduction remission to induction chemotherapy with a median overall survival of 12.50 months versus 7.23 months in the two groups. Furthermore, it was found that the ex vivo response to extracts and chemotherapeutics is heterogeneous and shows an exclusive pattern between the extracts, Anamu being the more effective in inducing cell death. The combination of extracts with chemotherapeutic agents showed synergistic or antagonistic effects in the patients' blasts. These results show that the ex vivo evaluation of the sensitivity to induction drugs using primary blasts from patients exhibits a correlation with the response to induction chemotherapy in patients. These analyses would allow establishing a system to predict response to treatment and determine ex vivo susceptibility to new therapies under development, among which is phytotherapeutics.
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24
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Tognon CE, Sears RC, Mills GB, Gray JW, Tyner JW. Ex Vivo Analysis of Primary Tumor Specimens for Evaluation of Cancer Therapeutics. ANNUAL REVIEW OF CANCER BIOLOGY-SERIES 2020; 5:39-57. [PMID: 34222745 DOI: 10.1146/annurev-cancerbio-043020-125955] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The use of ex vivo drug sensitivity testing to predict drug activity in individual patients has been actively explored for almost 50 years without delivering a generally useful predictive capability. However, extended failure should not be an indicator of futility. This is especially true in cancer research where ultimate success is often preceded by less successful attempts. For example, both immune- and genetic-based targeted therapies for cancer underwent numerous failed attempts before biological understanding, improved targets, and optimized drug development matured to facilitate an arsenal of transformational drugs. Similarly, the concept of directly assessing drug sensitivity of primary tumor biopsies-and the use of this information to help direct therapeutic approaches-has a long history with a definitive learning curve. In this review, we will survey the history of ex vivo testing as well as the current state of the art for this field. We will present an update on methodologies and approaches, describe the use of these technologies to test cutting-edge drug classes, and describe an increasingly nuanced understanding of tumor types and models for which this strategy is most likely to succeed. We will consider the relative strengths and weaknesses of predicting drug activity across the broad biological context of cancer patients and tumor types. This will include an analysis of the potential for ex vivo drug sensitivity testing to accurately predict drug activity within each of the biological hallmarks of cancer pathogenesis.
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Affiliation(s)
- Cristina E Tognon
- Division of Hematology & Medical Oncology, Oregon Health & Science University.,Knight Cancer Institute, Oregon Health & Science University
| | - Rosalie C Sears
- Knight Cancer Institute, Oregon Health & Science University.,Department of Molecular and Medical Genetics, Oregon Health and Science University.,Brenden-Colson Center for Pancreatic Care, Oregon Health and Science University
| | - Gordon B Mills
- Knight Cancer Institute, Oregon Health & Science University.,Brenden-Colson Center for Pancreatic Care, Oregon Health and Science University.,Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University
| | - Joe W Gray
- Knight Cancer Institute, Oregon Health & Science University.,Brenden-Colson Center for Pancreatic Care, Oregon Health and Science University.,Department of Biomedical Engineering, Oregon Health & Science University.,Center for Spatial Systems Biomedicine, Oregon Health & Science University
| | - Jeffrey W Tyner
- Division of Hematology & Medical Oncology, Oregon Health & Science University.,Knight Cancer Institute, Oregon Health & Science University.,Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University
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25
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Skånland SS, Karlsen L, Taskén K. B cell signalling pathways-New targets for precision medicine in chronic lymphocytic leukaemia. Scand J Immunol 2020; 92:e12931. [PMID: 32640099 DOI: 10.1111/sji.12931] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 06/15/2020] [Accepted: 07/02/2020] [Indexed: 01/16/2023]
Abstract
The B cell receptor (BCR) is a master regulator of B cells, controlling cellular processes such as proliferation, migration and survival. Cell signalling downstream of the BCR is aberrantly activated in the B cell malignancy chronic lymphocytic leukaemia (CLL), supporting the pathophysiology of the disease. This insight has led to development and approval of small molecule inhibitors that target components of the BCR pathway. These advances have greatly improved the management of CLL, but the disease remains incurable. This may partly be explained by the inter-patient heterogeneity of the disease, also when it comes to treatment responses. Precision medicine is therefore required to optimize treatment and move towards a cure. Here, we discuss how the introduction of BCR signalling inhibitors has facilitated the development of functional in vitro assays to guide clinical treatment decisions on use of the same therapeutic agents in individual patients. The cellular responses to these agents can be analysed in high-throughput assays such as dynamic BH3 profiling, phospho flow experiments and drug sensitivity screens to identify predictive biomarkers. This progress exemplifies the positive synergy between basal and translational research needed to optimize patient care.
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Affiliation(s)
- 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
| | - Linda Karlsen
- 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.,Institute of Clinical Medicine, 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.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
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26
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Manzella G, Schreck LD, Breunis WB, Molenaar J, Merks H, Barr FG, Sun W, Römmele M, Zhang L, Tchinda J, Ngo QA, Bode P, Delattre O, Surdez D, Rekhi B, Niggli FK, Schäfer BW, Wachtel M. Phenotypic profiling with a living biobank of primary rhabdomyosarcoma unravels disease heterogeneity and AKT sensitivity. Nat Commun 2020; 11:4629. [PMID: 32934208 PMCID: PMC7492191 DOI: 10.1038/s41467-020-18388-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 08/18/2020] [Indexed: 12/14/2022] Open
Abstract
Cancer therapy is currently shifting from broadly used cytotoxic drugs to patient-specific precision therapies. Druggable driver oncogenes, identified by molecular analyses, are present in only a subset of patients. Functional profiling of primary tumor cells could circumvent these limitations, but suitable platforms are unavailable for most cancer entities. Here, we describe an in vitro drug profiling platform for rhabdomyosarcoma (RMS), using a living biobank composed of twenty RMS patient-derived xenografts (PDX) for high-throughput drug testing. Optimized in vitro conditions preserve phenotypic and molecular characteristics of primary PDX cells and are compatible with propagation of cells directly isolated from patient tumors. Besides a heterogeneous spectrum of responses of largely patient-specific vulnerabilities, profiling with a large drug library reveals a strong sensitivity towards AKT inhibitors in a subgroup of RMS. Overall, our study highlights the feasibility of in vitro drug profiling of primary RMS for patient-specific treatment selection in a co-clinical setting. Patient-specific precision medicine approaches are important for future cancer therapies. Here, the authors show that functional drug profiling with Rhabdomyosarcoma cells isolated from PDX and primary patient tumors uncovers patient-specific vulnerabilities.
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Affiliation(s)
- Gabriele Manzella
- University Children's Hospital, Department of Oncology and Children's Research Center, Steinwiesstrasse 75, CH-8032, Zurich, Switzerland
| | - Leonie D Schreck
- University Children's Hospital, Department of Oncology and Children's Research Center, Steinwiesstrasse 75, CH-8032, Zurich, Switzerland
| | - Willemijn B Breunis
- University Children's Hospital, Department of Oncology and Children's Research Center, Steinwiesstrasse 75, CH-8032, Zurich, Switzerland.,Princess Máxima Center for Pediatric Oncology, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands
| | - Jan Molenaar
- Princess Máxima Center for Pediatric Oncology, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands
| | - Hans Merks
- Princess Máxima Center for Pediatric Oncology, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands
| | - Frederic G Barr
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Wenyue Sun
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Michaela Römmele
- University Children's Hospital, Department of Oncology and Children's Research Center, Steinwiesstrasse 75, CH-8032, Zurich, Switzerland
| | - Luduo Zhang
- University Children's Hospital, Department of Oncology and Children's Research Center, Steinwiesstrasse 75, CH-8032, Zurich, Switzerland
| | - Joelle Tchinda
- University Children's Hospital, Department of Oncology and Children's Research Center, Steinwiesstrasse 75, CH-8032, Zurich, Switzerland
| | - Quy A Ngo
- University Children's Hospital, Department of Oncology and Children's Research Center, Steinwiesstrasse 75, CH-8032, Zurich, Switzerland
| | - Peter Bode
- University Hospital Zurich, Institute of Surgical Pathology, Schmelzbergstrasse 12, CH-8091, Zurich, Switzerland
| | - Olivier Delattre
- France INSERM U830, Équipe Labellisé LNCC, PSL Université, SIREDO Oncology Centre, Institut Curie, Paris, France
| | - Didier Surdez
- France INSERM U830, Équipe Labellisé LNCC, PSL Université, SIREDO Oncology Centre, Institut Curie, Paris, France
| | - Bharat Rekhi
- Tata Memorial Hospital, Department of Pathology, Dr E.B. road, Parel, Mumbai, 400012, India
| | - Felix K Niggli
- University Children's Hospital, Department of Oncology and Children's Research Center, Steinwiesstrasse 75, CH-8032, Zurich, Switzerland
| | - Beat W Schäfer
- University Children's Hospital, Department of Oncology and Children's Research Center, Steinwiesstrasse 75, CH-8032, Zurich, Switzerland.
| | - Marco Wachtel
- University Children's Hospital, Department of Oncology and Children's Research Center, Steinwiesstrasse 75, CH-8032, Zurich, Switzerland
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27
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Anderson AN, McClanahan D, Jacobs J, Jeng S, Vigoda M, Blucher AS, Zheng C, Yoo YJ, Hale C, Ouyang X, Clayburgh D, Andersen P, Tyner JW, Bar A, Lucero OM, Leitenberger JJ, McWeeney SK, Kulesz-Martin M. Functional genomic analysis identifies drug targetable pathways in invasive and metastatic cutaneous squamous cell carcinoma. Cold Spring Harb Mol Case Stud 2020; 6:mcs.a005439. [PMID: 32843430 PMCID: PMC7476409 DOI: 10.1101/mcs.a005439] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 07/09/2020] [Indexed: 12/20/2022] Open
Abstract
Although cutaneous squamous cell carcinoma (cSCC) is treatable in the majority of cases, deadly invasive and metastatic cases do occur. To date there are neither reliable predictive biomarkers of disease progression nor FDA-approved targeted therapies as standard of care. To address these issues, we screened patient-derived primary cultured cells from invasive/metastatic cSCC with 107 small-molecule inhibitors. In-house bioinformatics tools were used to cross-analyze drug responses and DNA mutations in tumors detected by whole-exome sequencing (WES). Aberrations in molecular pathways with evidence of potential drug targets were identified, including the Eph-ephrin and neutrophil degranulation signaling pathways. Using a screening panel of siRNAs, we identified EPHA6 and EPHA7 as targets within the Eph-ephrin pathway responsible for mitigating decreased cell viability. These studies form a plausible foundation for detecting biomarkers of high-risk progressive disease applicable in dermatopathology and for patient-specific therapeutic options for invasive/metastatic cSCC.
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Affiliation(s)
- Ashley N Anderson
- Department of Dermatology, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Danielle McClanahan
- Department of Dermatology, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - James Jacobs
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University Knight Cancer Institute, Portland, Oregon 97239, USA
| | - Sophia Jeng
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University Knight Cancer Institute, Portland, Oregon 97239, USA.,Oregon Clinical and Translational Research Institute, Oregon Health and Science University, Portland, Oregon 97339, USA
| | - Myles Vigoda
- Department of Dermatology, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Aurora S Blucher
- Department of Cell, Developmental and Cancer Biology, Oregon Health and Science University Knight Cancer Institute, Portland, Oregon 97239, USA
| | - Christina Zheng
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University Knight Cancer Institute, Portland, Oregon 97239, USA
| | - Yeon Jung Yoo
- Department of Dermatology, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Carolyn Hale
- Department of Dermatology, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Xiaoming Ouyang
- Department of Dermatology, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Daniel Clayburgh
- Department of Otolaryngology, Oregon Health & Science University, Portland, Oregon 97239, USA.,Operative Care Division, Veterans Affairs Medical Center, Portland, Oregon 97239, USA
| | - Peter Andersen
- Department of Otolaryngology, Oregon Health & Science University, Portland, Oregon 97239, USA
| | - Jeffrey W Tyner
- Department of Cell, Developmental and Cancer Biology, Oregon Health and Science University Knight Cancer Institute, Portland, Oregon 97239, USA.,Division of Hematology and Medical Oncology, Oregon Health and Science University Knight Cancer Institute, Portland, Oregon 97239, USA
| | - Anna Bar
- Department of Dermatology, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Olivia M Lucero
- Department of Dermatology, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Justin J Leitenberger
- Department of Dermatology, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Shannon K McWeeney
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University Knight Cancer Institute, Portland, Oregon 97239, USA
| | - Molly Kulesz-Martin
- Department of Dermatology, Oregon Health and Science University, Portland, Oregon 97239, USA.,Department of Cell, Developmental and Cancer Biology, Oregon Health and Science University Knight Cancer Institute, Portland, Oregon 97239, USA
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28
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Popova AA, Dietrich S, Huber W, Reischl M, Peravali R, Levkin PA. Miniaturized Drug Sensitivity and Resistance Test on Patient-Derived Cells Using Droplet-Microarray. SLAS Technol 2020; 26:274-286. [PMID: 32791934 DOI: 10.1177/2472630320934432] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Testing the sensitivity of patient-derived tumor cells ex vivo can potentially help determining the appropriate treatment for each patient and spot the development of resistance to a given therapy. The number of cells obtainable from a biopsy is, however, often insufficient for performing ex vivo tests in conventional microtiter plates. Here, we introduce a novel Droplet-Microarray platform based on a hydrophilic-superhydrophobic patterned surface that enables screenings using only 100 cells and 30 picomoles of a drug per individual nanoliter-sized droplet. We demonstrate that the dose-response of as few as 100 primary patient-derived chronic lymphocytic leukemia (CLL) cells to anticancer compounds on the Droplet-Microarray platform resembles the dose-response obtained in 384-well plates requiring 20,000 tumor cells per experiment. The extremely miniaturized Droplet-Microarray platform thus carries great potential for ex vivo drug sensitivity and resistance tests on patient-derived tumor cells and potentially for implementing such tests in medical practice of precision medicine.
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Affiliation(s)
- Anna A Popova
- Karlsruhe Institute of Technology, Institute of Chemical and Biological Systems, Eggenstein-Leopoldshafen, Germany
| | - Sascha Dietrich
- National Center for Tumor Diseases, Heidelberg, Germany.,Medizinische Klinik V, University Hospital of Heidelberg, Heidelberg, Germany.,European Molecular Biology Laboratories (EMBL), Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
| | - Wolfgang Huber
- European Molecular Biology Laboratories (EMBL), Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
| | - Markus Reischl
- Karlsruhe Institute of Technology, Institute for Automation and Applied Informatics, Eggenstein-Leopoldshafen, Germany
| | - Ravindra Peravali
- Karlsruhe Institute of Technology, Institute of Chemical and Biological Systems, Eggenstein-Leopoldshafen, Germany
| | - Pavel A Levkin
- Karlsruhe Institute of Technology, Institute of Chemical and Biological Systems, Eggenstein-Leopoldshafen, Germany.,Karlsruhe Institute of Technology, Institute of Organic Chemistry, Karlsruhe, Germany
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29
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Genomic markers of midostaurin drug sensitivity in FLT3 mutated and FLT3 wild-type acute myeloid leukemia patients. Oncotarget 2020; 11:2807-2818. [PMID: 32754299 PMCID: PMC7381100 DOI: 10.18632/oncotarget.27656] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 06/05/2020] [Indexed: 11/25/2022] Open
Abstract
Acute myeloid leukemia (AML) is a heterogeneous malignancy with the most common genomic alterations in NPM1, DNMT3A, and FLT3. Midostaurin was the first FLT3 inhibitor FDA approved for AML and is standard of care for FLT3 mutant patients undergoing induction chemotherapy [1, 2]. As there is a spectrum of response, we hypothesized that biological factors beyond FLT3 could play a role in drug sensitivity and that select FLT3-ITD negative samples may also demonstrate sensitivity. Thus, we aimed to identify features that would predict response to midostaurin in FLT3 mutant and wild-type samples. We performed an ex vivo drug sensitivity screen on primary and relapsed AML samples with corresponding targeted sequencing and RNA sequencing. We observed a correlation between FLT3-ITD mutations and midostaurin sensitivity as expected and observed KRAS and TP53 mutations correlating with midostaurin resistance in FLT3-ITD negative samples. Further, we identified genes differentially expressed in sensitive vs. resistant samples independent of FLT3-ITD status. Within FLT3-ITD mutant samples, over-expression of RGL4, oncogene and regulator of the Ras-Raf-MEK-ERK cascade, distinguished resistant from sensitive samples. Overall, this study highlights the complexity underlying midostaurin response. And, our results suggest that therapies that target both FLT3 and MAPK/ERK signaling may help circumvent some cases of resistance.
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30
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Joshi SK, Qian K, Bisson WH, Watanabe-Smith K, Huang A, Bottomly D, Traer E, Tyner JW, McWeeney SK, Davare MA, Druker BJ, Tognon CE. Discovery and characterization of targetable NTRK point mutations in hematologic neoplasms. Blood 2020; 135:2159-2170. [PMID: 32315394 PMCID: PMC7290093 DOI: 10.1182/blood.2019003691] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 02/03/2020] [Indexed: 02/07/2023] Open
Abstract
Much of what is known about the neurotrophic receptor tyrosine kinase (NTRK) genes in cancer was revealed through identification and characterization of activating Trk fusions across many tumor types. A resurgence of interest in these receptors has emerged owing to the realization that they are promising therapeutic targets. The remarkable efficacy of pan-Trk inhibitors larotrectinib and entrectinib in clinical trials led to their accelerated, tissue-agnostic US Food and Drug Administration (FDA) approval for adult and pediatric patients with Trk-driven solid tumors. Despite our enhanced understanding of Trk biology in solid tumors, the importance of Trk signaling in hematological malignancies is underexplored and warrants further investigation. Herein, we describe mutations in NTRK2 and NTRK3 identified via deep sequencing of 185 patients with hematological malignancies. Ten patients contained a point mutation in NTRK2 or NTRK3; among these, we identified 9 unique point mutations. Of these 9 mutations, 4 were oncogenic (NTRK2A203T, NTRK2R458G, NTRK3E176D, and NTRK3L449F), determined via cytokine-independent cellular assays. Our data demonstrate that these mutations have transformative potential to promote downstream survival signaling and leukemogenesis. Specifically, the 3 mutations located within extracellular (ie, NTRK2A203T and NTRK3E176D) and transmembrane (ie, NTRK3L449F) domains increased receptor dimerization and cell-surface abundance. The fourth mutation, NTRK2R458G, residing in the juxtamembrane domain, activates TrkB via noncanonical mechanisms that may involve altered interactions between the mutant receptor and lipids in the surrounding environment. Importantly, these 4 activating mutations can be clinically targeted using entrectinib. Our findings contribute to ongoing efforts to define the mutational landscape driving hematological malignancies and underscore the utility of FDA-approved Trk inhibitors for patients with aggressive Trk-driven leukemias.
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Affiliation(s)
- Sunil K Joshi
- Knight Cancer Institute
- Department of Physiology and Pharmacology, School of Medicine, and
- Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR
| | | | - William H Bisson
- Knight Cancer Institute
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR; and
| | | | | | | | - Elie Traer
- Knight Cancer Institute
- Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR
- Department of Cell, Development, and Cancer Biology
| | - Jeffrey W Tyner
- Knight Cancer Institute
- Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR
- Department of Cell, Development, and Cancer Biology
| | - Shannon K McWeeney
- Knight Cancer Institute
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology
| | - Monika A Davare
- Department of Cell, Development, and Cancer Biology
- Papé Pediatric Research Institute
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, and
| | - Brian J Druker
- Knight Cancer Institute
- Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR
- Department of Cell, Development, and Cancer Biology
- Howard Hughes Medical Institute, Oregon Health & Science University, Portland, OR
| | - Cristina E Tognon
- Knight Cancer Institute
- Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR
- Howard Hughes Medical Institute, Oregon Health & Science University, Portland, OR
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31
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Watson NA, Cartwright TN, Lawless C, Cámara-Donoso M, Sen O, Sako K, Hirota T, Kimura H, Higgins JMG. Kinase inhibition profiles as a tool to identify kinases for specific phosphorylation sites. Nat Commun 2020; 11:1684. [PMID: 32245944 PMCID: PMC7125195 DOI: 10.1038/s41467-020-15428-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 03/06/2020] [Indexed: 01/08/2023] Open
Abstract
There are thousands of known cellular phosphorylation sites, but the paucity of ways to identify kinases for particular phosphorylation events remains a major roadblock for understanding kinase signaling. To address this, we here develop a generally applicable method that exploits the large number of kinase inhibitors that have been profiled on near-kinome-wide panels of protein kinases. The inhibition profile for each kinase provides a fingerprint that allows identification of unknown kinases acting on target phosphosites in cell extracts. We validate the method on diverse known kinase-phosphosite pairs, including histone kinases, EGFR autophosphorylation, and Integrin β1 phosphorylation by Src-family kinases. We also use our approach to identify the previously unknown kinases responsible for phosphorylation of INCENP at a site within a commonly phosphorylated motif in mitosis (a non-canonical target of Cyclin B-Cdk1), and of BCL9L at S915 (PKA). We show that the method has clear advantages over in silico and genetic screening.
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Affiliation(s)
- Nikolaus A Watson
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Tyrell N Cartwright
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Conor Lawless
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Marcos Cámara-Donoso
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Onur Sen
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Kosuke Sako
- The Cancer Institute, Japanese Foundation for Cancer Research, Koto, Tokyo, 135-8550, Japan
| | - Toru Hirota
- The Cancer Institute, Japanese Foundation for Cancer Research, Koto, Tokyo, 135-8550, Japan
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Kanagawa, 226-8503, Japan
| | - Jonathan M G Higgins
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.
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32
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Eide CA, Kurtz SE, Kaempf A, Long N, Agarwal A, Tognon CE, Mori M, Druker BJ, Chang BH, Danilov AV, Tyner JW. Simultaneous kinase inhibition with ibrutinib and BCL2 inhibition with venetoclax offers a therapeutic strategy for acute myeloid leukemia. Leukemia 2020; 34:2342-2353. [PMID: 32094466 DOI: 10.1038/s41375-020-0764-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 02/07/2020] [Accepted: 02/12/2020] [Indexed: 12/12/2022]
Abstract
Acute myeloid leukemia (AML) results from the enhanced proliferation and impaired differentiation of hematopoietic stem and progenitor cells. Using an ex vivo functional screening assay, we identified that the combination of the BTK inhibitor ibrutinib and BCL2 inhibitor venetoclax (IBR + VEN), currently in clinical trials for chronic lymphocytic leukemia (CLL), demonstrated enhanced efficacy on primary AML patient specimens, AML cell lines, and in a mouse xenograft model of AML. Expanded analyses among a large cohort of hematologic malignancies (n = 651 patients) revealed that IBR + VEN sensitivity associated with selected genetic and phenotypic features in both CLL and AML specimens. Among AML samples, 11q23 MLL rearrangements were highly sensitive to IBR + VEN. Analysis of differentially expressed genes with respect to IBR + VEN sensitivity indicated pathways preferentially enriched in patient samples with reduced ex vivo sensitivity, including IL-10 signaling. These findings suggest that IBR + VEN may represent an effective therapeutic option for patients with AML.
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Affiliation(s)
- Christopher A Eide
- Division of Hematology & Medical Oncology, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.,Howard Hughes Medical Institute, Portland, OR, USA
| | - Stephen E Kurtz
- Division of Hematology & Medical Oncology, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Andy Kaempf
- Biostatistics Shared Resource, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Nicola Long
- Division of Hematology & Medical Oncology, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Anupriya Agarwal
- Division of Hematology & Medical Oncology, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Cristina E Tognon
- Division of Hematology & Medical Oncology, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.,Howard Hughes Medical Institute, Portland, OR, USA
| | - Motomi Mori
- Biostatistics Shared Resource, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.,Portland State University and Oregon Health & Science University School of Public Health, Portland, OR, USA
| | - Brian J Druker
- Division of Hematology & Medical Oncology, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.,Howard Hughes Medical Institute, Portland, OR, USA
| | - Bill H Chang
- Division of Hematology & Medical Oncology, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Alexey V Danilov
- Division of Hematology & Medical Oncology, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Jeffrey W Tyner
- Division of Hematology & Medical Oncology, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA. .,Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR, USA.
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33
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Barnes EJ, Leonard J, Medeiros BC, Druker BJ, Tognon CE. Functional characterization of two rare BCR-FGFR1 + leukemias. Cold Spring Harb Mol Case Stud 2020; 6:mcs.a004838. [PMID: 31980503 PMCID: PMC7133745 DOI: 10.1101/mcs.a004838] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 01/08/2020] [Indexed: 12/19/2022] Open
Abstract
8p11 myeloproliferative syndrome (EMS) represents a unique World Health Organization (WHO)-classified hematologic malignancy defined by translocations of the FGFR1 receptor. The syndrome is a myeloproliferative neoplasm characterized by eosinophilia and lymphadenopathy, with risk of progression to either acute myeloid leukemia (AML) or T- or B-lymphoblastic lymphoma/leukemia. Within the EMS subtype, translocations between breakpoint cluster region (BCR) and fibroblast growth factor receptor 1 (FGFR1) have been shown to produce a dominant fusion protein that is notoriously resistant to tyrosine kinase inhibitors (TKIs). Here, we report two cases of BCR–FGFR1+ EMS identified via RNA sequencing (RNA-seq) and confirmed by fluorescence in situ hybridization (FISH). Sanger sequencing revealed that both cases harbored the exact same breakpoint. In the first case, the patient presented with AML-like disease, and in the second, the patient progressed to B-cell acute lymphoblastic leukemia (B-ALL). Additionally, we observed that that primary leukemia cells from Case 1 demonstrated sensitivity to the tyrosine kinase inhibitors ponatinib and dovitinib that can target FGFR1 kinase activity, whereas primary cells from Case 2 were resistant to both drugs. Taken together, these results suggest that some but not all BCR–FGFR1 fusion positive leukemias may respond to TKIs that target FGFR1 kinase activity.
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Affiliation(s)
- Evan J Barnes
- Division of Hematology and Medical Oncology, Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon 97239, USA
| | - Jessica Leonard
- Division of Hematology and Medical Oncology, Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon 97239, USA
| | - Bruno C Medeiros
- Department of Medicine-Hematology, Stanford University, Stanford, California 94305, USA
| | - Brian J Druker
- Division of Hematology and Medical Oncology, Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon 97239, USA.,Howard Hughes Medical Institute, Portland, Oregon 97239, USA
| | - Cristina E Tognon
- Department of Medicine-Hematology, Stanford University, Stanford, California 94305, USA.,Howard Hughes Medical Institute, Portland, Oregon 97239, USA
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34
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Gupta A, Gautam P, Wennerberg K, Aittokallio T. A normalized drug response metric improves accuracy and consistency of anticancer drug sensitivity quantification in cell-based screening. Commun Biol 2020; 3:42. [PMID: 31974521 PMCID: PMC6978361 DOI: 10.1038/s42003-020-0765-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 01/06/2020] [Indexed: 01/09/2023] Open
Abstract
Accurate quantification of drug effects is crucial for identifying pharmaceutically actionable cancer vulnerabilities. Current cell viability-based measurements often lead to biased response estimates due to varying growth rates and experimental artifacts that explain part of the inconsistency in high-throughput screening results. We developed an improved drug scoring model, normalized drug response (NDR), which makes use of both positive and negative control conditions to account for differences in cell growth rates, and experimental noise to better characterize drug-induced effects. We demonstrate an improved consistency and accuracy of NDR compared to existing metrics in assessing drug responses of cancer cells in various culture models and experimental setups. Notably, NDR reliably captures both toxicity and viability responses, and differentiates a wider spectrum of drug behavior, including lethal, growth-inhibitory and growth-stimulatory modes, based on a single viability readout. The method will therefore substantially reduce the time and resources required in cell-based drug sensitivity screening.
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Affiliation(s)
- Abhishekh Gupta
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Center for Quantitative Medicine, University of Connecticut School of Medicine, Farmington, CT, USA
| | - Prson Gautam
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Krister Wennerberg
- Institute for Molecular Medicine Finland (FIMM), 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.
| | - Tero Aittokallio
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland.
- Department of Mathematics and Statistics, University of Turku, Turku, Finland.
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35
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Popova AA, Levkin PA. Precision Medicine in Oncology: In Vitro Drug Sensitivity and Resistance Test (DSRT) for Selection of Personalized Anticancer Therapy. ADVANCED THERAPEUTICS 2020. [DOI: 10.1002/adtp.201900100] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Anna A. Popova
- Karlsruhe Institute of TechnologyInstitute of Toxicology and Genetics Hermann‐von‐Helmholtz‐Platz 1 76344 Eggenstein‐Leopoldshafen Germany
| | - Pavel A. Levkin
- Karlsruhe Institute of TechnologyInstitute of Toxicology and Genetics Hermann‐von‐Helmholtz‐Platz 1 76344 Eggenstein‐Leopoldshafen Germany
- Karlsruhe Institute of TechnologyInstitute of Organic Chemistry Fritz‐Haber Weg 6 76131 Karlsruhe Germany
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36
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Machine learning and data mining frameworks for predicting drug response in cancer: An overview and a novel in silico screening process based on association rule mining. Pharmacol Ther 2019; 203:107395. [DOI: 10.1016/j.pharmthera.2019.107395] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 07/11/2019] [Indexed: 12/20/2022]
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37
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Koromina M, Pandi MT, Patrinos GP. Rethinking Drug Repositioning and Development with Artificial Intelligence, Machine Learning, and Omics. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2019; 23:539-548. [PMID: 31651216 DOI: 10.1089/omi.2019.0151] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Pharmaceutical industry and the art and science of drug development are sorely in need of novel transformative technologies in the current age of digital health and artificial intelligence (AI). Often described as game-changing technologies, AI and machine learning algorithms have slowly but surely begun to revolutionize pharmaceutical industry and drug development over the past 5 years. In this expert review, we describe the most frequently used machine learning algorithms in drug development pipelines and the -omics databases well poised to support machine learning and drug discovery. Subsequently, we analyze the emerging new computational approaches to drug discovery and the in silico pipelines for drug repositioning and the synergies among -omics system sciences, AI and machine learning. As with system sciences, AI and machine learning embody a system scale and Big Data driven vision for drug discovery and development. We conclude with a future outlook on the ways in which machine learning approaches can be implemented to buttress and expedite drug discovery and precision medicine. As AI and machine learning are rapidly entering pharmaceutical industry and the art and science of drug development, we need to critically examine the attendant prospects and challenges to benefit patients and public health.
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Affiliation(s)
- Maria Koromina
- Laboratory of Pharmacogenomics and Individualized Therapy, Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece
| | - Maria-Theodora Pandi
- Laboratory of Pharmacogenomics and Individualized Therapy, Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece
| | - George P Patrinos
- Laboratory of Pharmacogenomics and Individualized Therapy, Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece.,Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, Abu Dhabi.,Zayed Center of Health Sciences, United Arab Emirates University, Al-Ain, Abu Dhabi
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38
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Kobayashi H, Lei C, Wu Y, Huang CJ, Yasumoto A, Jona M, Li W, Wu Y, Yalikun Y, Jiang Y, Guo B, Sun CW, Tanaka Y, Yamada M, Yatomi Y, Goda K. Intelligent whole-blood imaging flow cytometry for simple, rapid, and cost-effective drug-susceptibility testing of leukemia. LAB ON A CHIP 2019; 19:2688-2698. [PMID: 31287108 DOI: 10.1039/c8lc01370e] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Drug susceptibility (also called chemosensitivity) is an important criterion for developing a therapeutic strategy for various cancer types such as breast cancer and leukemia. Recently, functional assays such as high-content screening together with genomic analysis have been shown to be effective for predicting drug susceptibility, but their clinical applicability is poor since they are time-consuming (several days long), labor-intensive, and costly. Here we present a highly simple, rapid, and cost-effective liquid biopsy for ex vivo drug-susceptibility testing of leukemia. The method is based on an extreme-throughput (>1 million cells per second), label-free, whole-blood imaging flow cytometer with a deep convolutional autoencoder, enabling image-based identification of the drug susceptibility of every single white blood cell in whole blood within 24 hours by simply flowing a drug-treated whole blood sample as little as 500 μL into the imaging flow cytometer without labeling. Our results show that the method accurately evaluates the drug susceptibility of white blood cells from untreated patients with acute lymphoblastic leukemia. Our method holds promise for affordable precision medicine.
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39
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Kuusanmäki H, Leppä AM, Pölönen P, Kontro M, Dufva O, Deb D, Yadav B, Brück O, Kumar A, Everaus H, Gjertsen BT, Heinäniemi M, Porkka K, Mustjoki S, Heckman CA. Phenotype-based drug screening reveals association between venetoclax response and differentiation stage in acute myeloid leukemia. Haematologica 2019; 105:708-720. [PMID: 31296572 PMCID: PMC7049363 DOI: 10.3324/haematol.2018.214882] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 07/08/2019] [Indexed: 12/13/2022] Open
Affiliation(s)
- Heikki Kuusanmäki
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki .,Hematology Research Unit, Helsinki University Hospital Comprehensive Cancer Center, Helsinki
| | - Aino-Maija Leppä
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki
| | - Petri Pölönen
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Mika Kontro
- Hematology Research Unit, Helsinki University Hospital Comprehensive Cancer Center, Helsinki
| | - Olli Dufva
- Hematology Research Unit, Helsinki University Hospital Comprehensive Cancer Center, Helsinki
| | - Debashish Deb
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki
| | - Bhagwan Yadav
- Hematology Research Unit, Helsinki University Hospital Comprehensive Cancer Center, Helsinki
| | - Oscar Brück
- Hematology Research Unit, Helsinki University Hospital Comprehensive Cancer Center, Helsinki
| | - Ashwini Kumar
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki
| | - Hele Everaus
- Department of Hematology and Oncology, University of Tartu, Tartu, Estonia
| | - Bjørn T Gjertsen
- Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Merja Heinäniemi
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Kimmo Porkka
- Hematology Research Unit, Helsinki University Hospital Comprehensive Cancer Center, Helsinki
| | - Satu Mustjoki
- Hematology Research Unit, Helsinki University Hospital Comprehensive Cancer Center, Helsinki.,Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
| | - Caroline A Heckman
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki
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40
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Horibata S, Gui G, Lack J, DeStefano CB, Gottesman MM, Hourigan CS. Heterogeneity in refractory acute myeloid leukemia. Proc Natl Acad Sci U S A 2019; 116:10494-10503. [PMID: 31064876 PMCID: PMC6535032 DOI: 10.1073/pnas.1902375116] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Successful clinical remission to therapy for acute myeloid leukemia (AML) is required for long-term survival to be achieved. Despite trends in improved survival due to better supportive care, up to 40% of patients will have refractory disease, which has a poorly understood biology and carries a dismal prognosis. The development of effective treatment strategies has been hindered by a general lack of knowledge about mechanisms of chemotherapy resistance. Here, through transcriptomic analysis of 154 cases of treatment-naive AML, three chemorefractory patient groups with distinct expression profiles are identified. A classifier, four key refractory gene signatures (RG4), trained based on the expression profile of the highest risk refractory patients, validated in an independent cohort (n = 131), was prognostic for overall survival (OS) and refined an established 17-gene stemness score. Refractory subpopulations have differential expression in pathways involved in cell cycle, transcription, translation, metabolism, and/or stem cell properties. Ex vivo drug sensitivity to 122 small-molecule inhibitors revealed effective group-specific targeting of pathways among these three refractory groups. Gene expression profiling by RNA sequencing had a suboptimal ability to correctly predict those individuals resistant to conventional cytotoxic induction therapy, but could risk-stratify for OS and identify subjects most likely to have superior responses to a specific alternative therapy. Such personalized therapy may be studied prospectively in clinical trials.
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Affiliation(s)
- Sachi Horibata
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892;
| | - Gege Gui
- Laboratory of Myeloid Malignancies, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20814
| | - Justin Lack
- NIAID Collaborative Bioinformatics Resource, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD 21702
| | - Christin B DeStefano
- Laboratory of Myeloid Malignancies, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20814
- Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814
| | - Michael M Gottesman
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892;
| | - Christopher S Hourigan
- Laboratory of Myeloid Malignancies, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20814;
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41
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Rozanov D, Cheltsov A, Nilsen A, Boniface C, Forquer I, Korkola J, Gray J, Tyner J, Tognon CE, Mills GB, Spellman P. Targeting mitochondria in cancer therapy could provide a basis for the selective anti-cancer activity. PLoS One 2019; 14:e0205623. [PMID: 30908483 PMCID: PMC6433232 DOI: 10.1371/journal.pone.0205623] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 02/25/2019] [Indexed: 12/29/2022] Open
Abstract
To determine the target of the recently identified lead compound NSC130362 that is responsible for its selective anti-cancer efficacy and safety in normal cells, structure-activity relationship (SAR) studies were conducted. First, NSC13062 was validated as a starting compound for the described SAR studies in a variety of cell-based viability assays. Then, a small library of 1,4-naphthoquinines (1,4-NQs) and quinoline-5,8-diones was tested in cell viability assays using pancreatic cancer MIA PaCa-2 cells and normal human hepatocytes. The obtained data allowed us to select a set of both non-toxic compounds that preferentially induced apoptosis in cancer cells and toxic compounds that induced apoptosis in both cancer and normal cells. Anti-cancer activity of the selected non-toxic compounds was confirmed in viability assays using breast cancer HCC1187 cells. Consequently, the two sets of compounds were tested in multiple cell-based and in vitro activity assays to identify key factors responsible for the observed activity. Inhibition of the mitochondrial electron transfer chain (ETC) is a key distinguishing activity between the non-toxic and toxic compounds. Finally, we developed a mathematical model that was able to distinguish these two sets of compounds. The development of this model supports our conclusion that appropriate quantitative SAR (QSAR) models have the potential to be employed to develop anti-cancer compounds with improved potency while maintaining non-toxicity to normal cells.
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Affiliation(s)
- Dmitri Rozanov
- Department of Molecular and Medical Genetics, Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon, United States of America
- * E-mail:
| | - Anton Cheltsov
- Q-MOL LLC, San Diego, California, United States of America
| | - Aaron Nilsen
- Medicinal Chemistry Core, Oregon Health and Science University, Portland, Oregon, United States of America
| | - Christopher Boniface
- Department of Molecular and Medical Genetics, Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon, United States of America
| | - Isaac Forquer
- Chemistry Department, Portland State University, Portland, Oregon, United States of America
| | - James Korkola
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, Oregon, United States of America
| | - Joe Gray
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, Oregon, United States of America
| | - Jeffrey Tyner
- Department of Cell, Developmental and Cancer Biology, Oregon Health and Science University, Portland, Oregon, United States of America
| | - Cristina E. Tognon
- Department of Cell, Developmental and Cancer Biology, Oregon Health and Science University, Portland, Oregon, United States of America
- Howard Hughes Medical Institute, Portland, Oregon, United States of America
- Division of Hematology & Medical Oncology, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Gordon B. Mills
- Department of Cell, Developmental and Cancer Biology, Oregon Health and Science University, Portland, Oregon, United States of America
| | - Paul Spellman
- Department of Molecular and Medical Genetics, Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon, United States of America
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42
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Edwards DK, Watanabe-Smith K, Rofelty A, Damnernsawad A, Laderas T, Lamble A, Lind EF, Kaempf A, Mori M, Rosenberg M, d'Almeida A, Long N, Agarwal A, Sweeney DT, Loriaux M, McWeeney SK, Tyner JW. CSF1R inhibitors exhibit antitumor activity in acute myeloid leukemia by blocking paracrine signals from support cells. Blood 2019; 133:588-599. [PMID: 30425048 PMCID: PMC6367650 DOI: 10.1182/blood-2018-03-838946] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 11/09/2018] [Indexed: 12/14/2022] Open
Abstract
To identify new therapeutic targets in acute myeloid leukemia (AML), we performed small-molecule and small-interfering RNA (siRNA) screens of primary AML patient samples. In 23% of samples, we found sensitivity to inhibition of colony-stimulating factor 1 (CSF1) receptor (CSF1R), a receptor tyrosine kinase responsible for survival, proliferation, and differentiation of myeloid-lineage cells. Sensitivity to CSF1R inhibitor GW-2580 was found preferentially in de novo and favorable-risk patients, and resistance to GW-2580 was associated with reduced overall survival. Using flow cytometry, we discovered that CSF1R is not expressed on the majority of leukemic blasts but instead on a subpopulation of supportive cells. Comparison of CSF1R-expressing cells in AML vs healthy donors by mass cytometry revealed expression of unique cell-surface markers. The quantity of CSF1R-expressing cells correlated with GW-2580 sensitivity. Exposure of primary AML patient samples to a panel of recombinant cytokines revealed that CSF1R inhibitor sensitivity correlated with a growth response to CSF1R ligand, CSF1, and other cytokines, including hepatocyte growth factor (HGF). The addition of CSF1 increased the secretion of HGF and other cytokines in conditioned media from AML patient samples, whereas adding GW-2580 reduced their secretion. In untreated cells, HGF levels correlated significantly with GW-2580 sensitivity. Finally, recombinant HGF and HS-5-conditioned media rescued cell viability after GW-2580 treatment in AML patient samples. Our results suggest that CSF1R-expressing cells support the bulk leukemia population through the secretion of HGF and other cytokines. This study identifies CSF1R as a novel therapeutic target of AML and provides a mechanism of paracrine cytokine/growth factor signaling in this disease.
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Affiliation(s)
- David K Edwards
- Department of Cell, Developmental & Cancer Biology, Knight Cancer Institute
| | | | - Angela Rofelty
- Division of Hematology and Medical Oncology, Knight Cancer Institute
| | | | - Ted Laderas
- Department of Medical Informatics and Clinical Epidemiology, and
| | - Adam Lamble
- Division of Hematology and Medical Oncology, Knight Cancer Institute
| | - Evan F Lind
- Division of Hematology and Medical Oncology, Knight Cancer Institute
| | - Andy Kaempf
- Biostatistics Shared Resource, Knight Cancer Institute, Oregon Health & Science University, Portland, OR; and
| | - Motomi Mori
- Biostatistics Shared Resource, Knight Cancer Institute, Oregon Health & Science University, Portland, OR; and
- School of Public Health, Oregon Health & Science University-Portland State University, Portland, OR
| | - Mara Rosenberg
- Division of Hematology and Medical Oncology, Knight Cancer Institute
| | - Amanda d'Almeida
- Division of Hematology and Medical Oncology, Knight Cancer Institute
| | - Nicola Long
- Division of Hematology and Medical Oncology, Knight Cancer Institute
| | - Anupriya Agarwal
- Division of Hematology and Medical Oncology, Knight Cancer Institute
| | | | - Marc Loriaux
- Division of Hematology and Medical Oncology, Knight Cancer Institute
| | | | - Jeffrey W Tyner
- Department of Cell, Developmental & Cancer Biology, Knight Cancer Institute
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43
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Jaiswal A, Yadav B, Wennerberg K, Aittokallio T. Integrated Analysis of Drug Sensitivity and Selectivity to Predict Synergistic Drug Combinations and Target Coaddictions in Cancer. Methods Mol Biol 2019; 1888:205-217. [PMID: 30519949 DOI: 10.1007/978-1-4939-8891-4_12] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
High-throughput drug sensitivity testing provides a powerful phenotypic profiling approach to identify effective drug candidates for individual cell lines or patient-derived samples. Here, we describe an experimental-computational pipeline, named target addiction scoring (TAS), which mathematically transforms the drug response profiles into target addiction signatures, and thereby provides a ranking of potential therapeutic targets according to their functional importance in a particular cancer sample. The TAS pipeline makes use of drug polypharmacology to integrate the drug sensitivity and selectivity profiles through systems-wide interconnection networks between drugs and their targets, including both primary protein targets as well as secondary off-targets. We show how the TAS pipeline enables one to identify not only single-target addictions but also combinatorial coaddictions among targets that often underlie synergistic drug combinations.
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Affiliation(s)
- Alok Jaiswal
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Bhagwan Yadav
- Hematology Research Unit Helsinki (HRUH), University of Helsinki, Helsinki, Finland
| | - Krister Wennerberg
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Tero Aittokallio
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland.
- Department of Mathematics and Statistics, University of Turku, Turku, Finland.
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44
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Zhang H, Paliga A, Hobbs E, Moore S, Olson S, Long N, Dao KHT, Tyner JW. Two myeloid leukemia cases with rare FLT3 fusions. Cold Spring Harb Mol Case Stud 2018; 4:a003079. [PMID: 30559310 PMCID: PMC6318770 DOI: 10.1101/mcs.a003079] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 08/06/2018] [Indexed: 01/01/2023] Open
Abstract
Genetic rearrangements involving FLT3 are rare and only recently have been detected in myeloid/lymphoid neoplasms associated with eosinophilia (MLN-eos) and chronic myeloproliferative disorders. Here we report two cases with FLT3 fusions in patients demonstrating mixed features of myelodysplastic/myeloproliferative neoplasms. In the first case, FLT3 was fused with a new fusion partner MYO18A in a patient with marrow features most consistent with atypical chronic myeloid leukemia; the second case involving ETV6-FLT3 fusion was observed in a case with bone marrow features most consistent with chronic myelomonocytic leukemia. Notably, we observed that samples from both patients demonstrated FLT3 inhibitor (quizartinib and sorafenib) sensitivity in ex vivo drug screening assay.
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Affiliation(s)
- Haijiao Zhang
- Department of Cell, Developmental and Cancer Biology, Oregon Health and Science University, Knight Cancer Institute, Portland, Oregon 97239, USA
| | - Aleksandra Paliga
- Division of Hematology and Medical Oncology, Oregon Health and Science University, Knight Cancer Institute, Portland, Oregon 97239, USA
| | - Evie Hobbs
- Division of Hematology and Medical Oncology, Oregon Health and Science University, Knight Cancer Institute, Portland, Oregon 97239, USA
| | - Stephen Moore
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Knight Cancer Institute, Portland, Oregon 97239, USA
| | - Susan Olson
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Knight Cancer Institute, Portland, Oregon 97239, USA
| | - Nicola Long
- Department of Cell, Developmental and Cancer Biology, Oregon Health and Science University, Knight Cancer Institute, Portland, Oregon 97239, USA
| | - Kim-Hien T Dao
- Division of Hematology and Medical Oncology, Oregon Health and Science University, Knight Cancer Institute, Portland, Oregon 97239, USA
| | - Jeffrey W Tyner
- Department of Cell, Developmental and Cancer Biology, Oregon Health and Science University, Knight Cancer Institute, Portland, Oregon 97239, USA
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45
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Tyner JW, Tognon CE, Bottomly D, Wilmot B, Kurtz SE, Savage SL, Long N, Schultz AR, Traer E, Abel M, Agarwal A, Blucher A, Borate U, Bryant J, Burke R, Carlos A, Carpenter R, Carroll J, Chang BH, Coblentz C, d'Almeida A, Cook R, Danilov A, Dao KHT, Degnin M, Devine D, Dibb J, Edwards DK, Eide CA, English I, Glover J, Henson R, Ho H, Jemal A, Johnson K, Johnson R, Junio B, Kaempf A, Leonard J, Lin C, Liu SQ, Lo P, Loriaux MM, Luty S, Macey T, MacManiman J, Martinez J, Mori M, Nelson D, Nichols C, Peters J, Ramsdill J, Rofelty A, Schuff R, Searles R, Segerdell E, Smith RL, Spurgeon SE, Sweeney T, Thapa A, Visser C, Wagner J, Watanabe-Smith K, Werth K, Wolf J, White L, Yates A, Zhang H, Cogle CR, Collins RH, Connolly DC, Deininger MW, Drusbosky L, Hourigan CS, Jordan CT, Kropf P, Lin TL, Martinez ME, Medeiros BC, Pallapati RR, Pollyea DA, Swords RT, Watts JM, Weir SJ, Wiest DL, Winters RM, McWeeney SK, Druker BJ. Functional genomic landscape of acute myeloid leukaemia. Nature 2018; 562:526-531. [PMID: 30333627 PMCID: PMC6280667 DOI: 10.1038/s41586-018-0623-z] [Citation(s) in RCA: 731] [Impact Index Per Article: 121.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 08/14/2018] [Indexed: 01/08/2023]
Abstract
The implementation of targeted therapies for acute myeloid leukaemia (AML) has been challenging because of the complex mutational patterns within and across patients as well as a dearth of pharmacologic agents for most mutational events. Here we report initial findings from the Beat AML programme on a cohort of 672 tumour specimens collected from 562 patients. We assessed these specimens using whole-exome sequencing, RNA sequencing and analyses of ex vivo drug sensitivity. Our data reveal mutational events that have not previously been detected in AML. We show that the response to drugs is associated with mutational status, including instances of drug sensitivity that are specific to combinatorial mutational events. Integration with RNA sequencing also revealed gene expression signatures, which predict a role for specific gene networks in the drug response. Collectively, we have generated a dataset-accessible through the Beat AML data viewer (Vizome)-that can be leveraged to address clinical, genomic, transcriptomic and functional analyses of the biology of AML.
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Affiliation(s)
- Jeffrey W Tyner
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Cristina E Tognon
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
- Howard Hughes Medical Institute, Portland, OR, USA
| | - Daniel Bottomly
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, USA
| | - Beth Wilmot
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, USA
- Oregon Clinical & Translational Research Institute, Oregon Health & Science University, Portland, OR, USA
| | - Stephen E Kurtz
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Samantha L Savage
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Nicola Long
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Anna Reister Schultz
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Elie Traer
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Melissa Abel
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Anupriya Agarwal
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Aurora Blucher
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, USA
| | - Uma Borate
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Jade Bryant
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Russell Burke
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Amy Carlos
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Integrated Genomics Laboratories, Oregon Health & Science University, Portland, OR, USA
| | - Richie Carpenter
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Joseph Carroll
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Technology Transfer & Business Development, Oregon Health & Science University, Portland, OR, USA
| | - Bill H Chang
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology and Oncology, Department of Pediatrics, Oregon Health & Science University, Portland, OR, USA
| | - Cody Coblentz
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Amanda d'Almeida
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Rachel Cook
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Alexey Danilov
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Kim-Hien T Dao
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Michie Degnin
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Deirdre Devine
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - James Dibb
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - David K Edwards
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Christopher A Eide
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
- Howard Hughes Medical Institute, Portland, OR, USA
| | - Isabel English
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Jason Glover
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology and Oncology, Department of Pediatrics, Oregon Health & Science University, Portland, OR, USA
| | - Rachel Henson
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Integrated Genomics Laboratories, Oregon Health & Science University, Portland, OR, USA
| | - Hibery Ho
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Abdusebur Jemal
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology and Oncology, Department of Pediatrics, Oregon Health & Science University, Portland, OR, USA
| | - Kara Johnson
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Ryan Johnson
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Brian Junio
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Andy Kaempf
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Biostatistics Shared Resource, Oregon Health & Science University, Portland, OR, USA
| | - Jessica Leonard
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Chenwei Lin
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Integrated Genomics Laboratories, Oregon Health & Science University, Portland, OR, USA
| | - Selina Qiuying Liu
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Pierrette Lo
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Marc M Loriaux
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Dapartment of Pathology, Oregon Health & Science University, Portland, OR, USA
| | - Samuel Luty
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Tara Macey
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Jason MacManiman
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Jacqueline Martinez
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Motomi Mori
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Biostatistics Shared Resource, Oregon Health & Science University, Portland, OR, USA
- Oregon Health & Science University-Portland State University School of Public Health, Portland, OR, USA
| | - Dylan Nelson
- High-Throughput Screening Services Laboratory, Oregon State University, Corvalis, OR, USA
| | - Ceilidh Nichols
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Jill Peters
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Justin Ramsdill
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, USA
- Oregon Clinical & Translational Research Institute, Oregon Health & Science University, Portland, OR, USA
| | - Angela Rofelty
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Robert Schuff
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, USA
- Oregon Clinical & Translational Research Institute, Oregon Health & Science University, Portland, OR, USA
| | - Robert Searles
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Integrated Genomics Laboratories, Oregon Health & Science University, Portland, OR, USA
| | - Erik Segerdell
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, USA
| | - Rebecca L Smith
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Stephen E Spurgeon
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Tyler Sweeney
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Aashis Thapa
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Corinne Visser
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Jake Wagner
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Kevin Watanabe-Smith
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Kristen Werth
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Joelle Wolf
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology and Oncology, Department of Pediatrics, Oregon Health & Science University, Portland, OR, USA
| | - Libbey White
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, USA
| | - Amy Yates
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, USA
- Oregon Clinical & Translational Research Institute, Oregon Health & Science University, Portland, OR, USA
| | - Haijiao Zhang
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Christopher R Cogle
- Department of Medicine, Division of Hematology and Oncology, University of Florida, Gainesville, FL, USA
| | - Robert H Collins
- Department of Internal Medicine/Hematology Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Denise C Connolly
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, USA
- Fox Chase Cancer Center Biosample Repository Facility, Philadelphia, PA, USA
| | - Michael W Deininger
- Division of Hematology & Hematologic Malignancies, Department of Internal Medicine, University of Utah, Salt Lake City, UT, USA
| | - Leylah Drusbosky
- Department of Medicine, Division of Hematology and Oncology, University of Florida, Gainesville, FL, USA
| | - Christopher S Hourigan
- National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Craig T Jordan
- Division of Hematology, University of Colorado, Denver, CO, USA
| | - Patricia Kropf
- Bone Marrow Transplant Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Tara L Lin
- Division of Hematologic Malignancies & Cellular Therapeutics, University of Kansas, Kansas City, KS, USA
| | - Micaela E Martinez
- Clinical Research Services, University of Miami Sylvester Comprehensive Cancer Center, Miami, FL, USA
| | - Bruno C Medeiros
- Department of Medicine-Hematology, Stanford University, Stanford, CA, USA
| | - Rachel R Pallapati
- Clinical Research Services, University of Miami Sylvester Comprehensive Cancer Center, Miami, FL, USA
| | | | - Ronan T Swords
- Department of Hematology, University of Miami Sylvester Comprehensive Cancer Center, Miami, FL, USA
| | - Justin M Watts
- Department of Hematology, University of Miami Sylvester Comprehensive Cancer Center, Miami, FL, USA
| | - Scott J Weir
- Department of Toxicology, Pharmacology and Therapeutics, University of Kansas Medical Center, Kansas City, KS, USA
- Department of Medicine, Division of Medical Oncology, University of Kansas Medical Center, Kansas City, KS, USA
| | - David L Wiest
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Ryan M Winters
- Fox Chase Cancer Center Biosample Repository Facility, Philadelphia, PA, USA
| | - Shannon K McWeeney
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, USA.
- Oregon Clinical & Translational Research Institute, Oregon Health & Science University, Portland, OR, USA.
| | - Brian J Druker
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA.
- Howard Hughes Medical Institute, Portland, OR, USA.
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46
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Bassan R, Bourquin JP, DeAngelo DJ, Chiaretti S. New Approaches to the Management of Adult Acute Lymphoblastic Leukemia. J Clin Oncol 2018; 36:JCO2017773648. [PMID: 30240326 DOI: 10.1200/jco.2017.77.3648] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Traditional treatment regimens for adult acute lymphoblastic leukemia, including allogeneic hematopoietic cell transplantation, result in an overall survival of approximately 40%, a figure hardly comparable with the extraordinary 80% to 90% cure rate currently reported in children. When translated to the adult setting, modern pediatric-type regimens improve the survival to approximately 60% in young adults. The addition of tyrosine kinase inhibitors for patients with Philadelphia chromosome-positive disease and the measurement of minimal residual disease to guide risk stratification and postremission approaches has led to additional improvements in outcomes. Relapsed disease and treatment toxicity-sparing no patient but representing a major concern especially in the elderly-are the most critical current issues awaiting further therapeutic advancement. Recently, there has been considerable progress in understanding the disease biology, specifically the Philadelphia-like signature, as well as other high-risk subgroups. In addition, there are several new agents that will undoubtedly contribute to additional improvement in the current outcomes. The most promising agents are monoclonal antibodies, immunomodulators, and chimeric antigen receptor T cells, and, to a lesser extent, several new drugs targeting key molecular pathways involved in leukemic cell growth and proliferation. This review examines the evidence supporting the increasing role of the new therapeutic tools and treatment options in different disease subgroups, including frontline and relapsed or refractory disease. It is now possible to define the best individual approach on the basis of the emerging concepts of precision medicine.
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Affiliation(s)
- Renato Bassan
- Renato Bassan, Ospedale dell'Angelo, Mestre-Venezia; Sabina Chiaretti, "Sapienza" University, Rome, Italy; Jean-Pierre Bourquin, University Children's Hospital, Zurich, Switzerland; and Daniel J. DeAngelo, Dana-Farber Cancer Institute, Boston, MA
| | - Jean-Pierre Bourquin
- Renato Bassan, Ospedale dell'Angelo, Mestre-Venezia; Sabina Chiaretti, "Sapienza" University, Rome, Italy; Jean-Pierre Bourquin, University Children's Hospital, Zurich, Switzerland; and Daniel J. DeAngelo, Dana-Farber Cancer Institute, Boston, MA
| | - Daniel J DeAngelo
- Renato Bassan, Ospedale dell'Angelo, Mestre-Venezia; Sabina Chiaretti, "Sapienza" University, Rome, Italy; Jean-Pierre Bourquin, University Children's Hospital, Zurich, Switzerland; and Daniel J. DeAngelo, Dana-Farber Cancer Institute, Boston, MA
| | - Sabina Chiaretti
- Renato Bassan, Ospedale dell'Angelo, Mestre-Venezia; Sabina Chiaretti, "Sapienza" University, Rome, Italy; Jean-Pierre Bourquin, University Children's Hospital, Zurich, Switzerland; and Daniel J. DeAngelo, Dana-Farber Cancer Institute, Boston, MA
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47
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Differentiation-state plasticity is a targetable resistance mechanism in basal-like breast cancer. Nat Commun 2018; 9:3815. [PMID: 30232459 PMCID: PMC6145927 DOI: 10.1038/s41467-018-05729-w] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 07/24/2018] [Indexed: 01/03/2023] Open
Abstract
Intratumoral heterogeneity in cancers arises from genomic instability and epigenomic plasticity and is associated with resistance to cytotoxic and targeted therapies. We show here that cell-state heterogeneity, defined by differentiation-state marker expression, is high in triple-negative and basal-like breast cancer subtypes, and that drug tolerant persister (DTP) cell populations with altered marker expression emerge during treatment with a wide range of pathway-targeted therapeutic compounds. We show that MEK and PI3K/mTOR inhibitor-driven DTP states arise through distinct cell-state transitions rather than by Darwinian selection of preexisting subpopulations, and that these transitions involve dynamic remodeling of open chromatin architecture. Increased activity of many chromatin modifier enzymes, including BRD4, is observed in DTP cells. Co-treatment with the PI3K/mTOR inhibitor BEZ235 and the BET inhibitor JQ1 prevents changes to the open chromatin architecture, inhibits the acquisition of a DTP state, and results in robust cell death in vitro and xenograft regression in vivo. Resistance to therapy can be driven by intratumoral heterogeneity. Here, the authors show that drug tolerant persistent cell populations emerge during treatment, and these emergent populations arise through epigenetically mediated cell state transitions rather than sub population selection.
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48
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Ouyang X, Barling A, Lesch A, Tyner JW, Choonoo G, Zheng C, Jeng S, West TM, Clayburgh D, Courtneidge SA, McWeeney SK, Kulesz-Martin M. Induction of anaplastic lymphoma kinase (ALK) as a novel mechanism of EGFR inhibitor resistance in head and neck squamous cell carcinoma patient-derived models. Cancer Biol Ther 2018; 19:921-933. [PMID: 29856687 PMCID: PMC6300392 DOI: 10.1080/15384047.2018.1451285] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 03/07/2018] [Indexed: 01/09/2023] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) currently only has one FDA-approved cancer intrinsic targeted therapy, the epidermal growth factor receptor (EGFR) inhibitor cetuximab, to which only approximately 10% of tumors are sensitive. In order to extend therapy options, we subjected patient-derived HNSCC cells to small-molecule inhibitor and siRNA screens, first, to find effective combination therapies with an EGFR inhibitor, and second, to determine a potential mechanistic basis for repurposing the FDA approved agents for HNSCC. The combinations of EGFR inhibitor with anaplastic lymphoma kinase (ALK) inhibitors demonstrated synergy at the highest ratio in our cohort, 4/8 HNSCC patients' derived tumor cells, and this corresponded with an effectiveness of siRNA targeting ALK combined with the EGFR inhibitor gefitinib. Co-targeting EGFR and ALK decreased HNSCC cell number and colony formation ability and increased annexin V staining. Because ALK expression is low and ALK fusions are infrequent in HNSCC, we hypothesized that gefitinib treatment could induce ALK expression. We show that ALK expression was induced in HNSCC patient-derived cells both in 2D and 3D patient-derived cell culture models, and in patient-derived xenografts in mice. Four different ALK inhibitors, including two (ceritinib and brigatinib) FDA approved for lung cancer, were effective in combination with gefitinib. Together, we identified induction of ALK by EGFR inhibitor as a novel mechanism potentially relevant to resistance to EGFR inhibitor, a high ratio of response of HNSCC patient-derived tumor cells to a combination of ALK and EGFR inhibitors, and applicability of repurposing ALK inhibitors to HNSCC that lack ALK aberrations.
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Affiliation(s)
- Xiaoming Ouyang
- Department of Dermatology, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd., Portland, Oregon
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd., Portland, Oregon
| | - Ashley Barling
- Department of Dermatology, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd., Portland, Oregon
| | - Aletha Lesch
- Department of Dermatology, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd., Portland, Oregon
| | - Jeffrey W. Tyner
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd., Portland, Oregon
- Division of Hematology and Medical Oncology, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd., Portland, Oregon
- Knight Cancer Institute, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd., Portland, Oregon
| | - Gabrielle Choonoo
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics & Clinical Epidemiology, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd., Portland, Oregon
| | - Christina Zheng
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics & Clinical Epidemiology, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd., Portland, Oregon
| | - Sophia Jeng
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics & Clinical Epidemiology, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd., Portland, Oregon
| | - Toni M. West
- Department of Pharmacology, University of California at Davis, 451 Health Science Dr., Davis, California
| | - Daniel Clayburgh
- Department of Otolaryngology-Head and Neck Surgery, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd., Portland, Oregon
- Operative Care Division, Portland VA Health Care System, 3710 SW US Veterans Hospital Rd., Portland, Oregon
| | - Sara A. Courtneidge
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd., Portland, Oregon
- Knight Cancer Institute, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd., Portland, Oregon
| | - Shannon K. McWeeney
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics & Clinical Epidemiology, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd., Portland, Oregon
| | - Molly Kulesz-Martin
- Department of Dermatology, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd., Portland, Oregon
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd., Portland, Oregon
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49
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Ali M, Aittokallio T. Machine learning and feature selection for drug response prediction in precision oncology applications. Biophys Rev 2018; 11:31-39. [PMID: 30097794 PMCID: PMC6381361 DOI: 10.1007/s12551-018-0446-z] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 07/22/2018] [Indexed: 02/07/2023] Open
Abstract
In-depth modeling of the complex interplay among multiple omics data measured from cancer cell lines or patient tumors is providing new opportunities toward identification of tailored therapies for individual cancer patients. Supervised machine learning algorithms are increasingly being applied to the omics profiles as they enable integrative analyses among the high-dimensional data sets, as well as personalized predictions of therapy responses using multi-omics panels of response-predictive biomarkers identified through feature selection and cross-validation. However, technical variability and frequent missingness in input "big data" require the application of dedicated data preprocessing pipelines that often lead to some loss of information and compressed view of the biological signal. We describe here the state-of-the-art machine learning methods for anti-cancer drug response modeling and prediction and give our perspective on further opportunities to make better use of high-dimensional multi-omics profiles along with knowledge about cancer pathways targeted by anti-cancer compounds when predicting their phenotypic responses.
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Affiliation(s)
- Mehreen Ali
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, FI-00290, Helsinki, Finland.,Helsinki Institute for Information Technology (HIIT), Aalto University, FI-02150, Espoo, Finland
| | - Tero Aittokallio
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, FI-00290, Helsinki, Finland. .,Helsinki Institute for Information Technology (HIIT), Aalto University, FI-02150, Espoo, Finland. .,Department of Mathematics and Statistics, University of Turku, FI-20014, Turku, Finland.
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50
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Kodack DP, Farago AF, Dastur A, Held MA, Dardaei L, Friboulet L, von Flotow F, Damon LJ, Lee D, Parks M, Dicecca R, Greenberg M, Kattermann KE, Riley AK, Fintelmann FJ, Rizzo C, Piotrowska Z, Shaw AT, Gainor JF, Sequist LV, Niederst MJ, Engelman JA, Benes CH. Primary Patient-Derived Cancer Cells and Their Potential for Personalized Cancer Patient Care. Cell Rep 2018; 21:3298-3309. [PMID: 29241554 PMCID: PMC5745232 DOI: 10.1016/j.celrep.2017.11.051] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 09/28/2017] [Accepted: 11/14/2017] [Indexed: 01/27/2023] Open
Abstract
Personalized cancer therapy is based on a patient's tumor lineage, histopathology, expression analyses, and/or tumor DNA or RNA analysis. Here, we aim to develop an in vitro functional assay of a patient's living cancer cells that could complement these approaches. We present methods for developing cell cultures from tumor biopsies and identify the types of samples and culture conditions associated with higher efficiency of model establishment. Toward the application of patient-derived cell cultures for personalized care, we established an immunofluorescence-based functional assay that quantifies cancer cell responses to targeted therapy in mixed cell cultures. Assaying patient-derived lung cancer cultures with this method showed promise in modeling patient response for diagnostic use. This platform should allow for the development of co-clinical trial studies to prospectively test the value of drug profiling on tumor-biopsy-derived cultures to direct patient care.
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Affiliation(s)
- David P Kodack
- Massachusetts General Hospital Cancer Center, Boston, MA 02129, USA
| | - Anna F Farago
- Massachusetts General Hospital Cancer Center, Boston, MA 02129, USA
| | - Anahita Dastur
- Massachusetts General Hospital Cancer Center, Boston, MA 02129, USA
| | - Matthew A Held
- Massachusetts General Hospital Cancer Center, Boston, MA 02129, USA
| | - Leila Dardaei
- Massachusetts General Hospital Cancer Center, Boston, MA 02129, USA
| | - Luc Friboulet
- Massachusetts General Hospital Cancer Center, Boston, MA 02129, USA
| | | | - Leah J Damon
- Massachusetts General Hospital Cancer Center, Boston, MA 02129, USA
| | - Dana Lee
- Massachusetts General Hospital Cancer Center, Boston, MA 02129, USA
| | - Melissa Parks
- Massachusetts General Hospital Cancer Center, Boston, MA 02129, USA
| | - Richard Dicecca
- Massachusetts General Hospital Cancer Center, Boston, MA 02129, USA
| | - Max Greenberg
- Massachusetts General Hospital Cancer Center, Boston, MA 02129, USA
| | | | - Amanda K Riley
- Massachusetts General Hospital Cancer Center, Boston, MA 02129, USA
| | | | - Coleen Rizzo
- Massachusetts General Hospital Cancer Center, Boston, MA 02129, USA
| | - Zofia Piotrowska
- Massachusetts General Hospital Cancer Center, Boston, MA 02129, USA
| | - Alice T Shaw
- Massachusetts General Hospital Cancer Center, Boston, MA 02129, USA
| | - Justin F Gainor
- Massachusetts General Hospital Cancer Center, Boston, MA 02129, USA
| | - Lecia V Sequist
- Massachusetts General Hospital Cancer Center, Boston, MA 02129, USA
| | | | | | - Cyril H Benes
- Massachusetts General Hospital Cancer Center, Boston, MA 02129, USA.
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