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Balasooriya ER, Madhusanka D, López-Palacios TP, Eastmond RJ, Jayatunge D, Owen JJ, Gashler JS, Egbert CM, Bulathsinghalage C, Liu L, Piccolo SR, Andersen JL. Integrating Clinical Cancer and PTM Proteomics Data Identifies a Mechanism of ACK1 Kinase Activation. Mol Cancer Res 2024; 22:137-151. [PMID: 37847650 PMCID: PMC10831333 DOI: 10.1158/1541-7786.mcr-23-0153] [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: 03/09/2023] [Revised: 08/17/2023] [Accepted: 10/13/2023] [Indexed: 10/19/2023]
Abstract
Beyond the most common oncogenes activated by mutation (mut-drivers), there likely exists a variety of low-frequency mut-drivers, each of which is a possible frontier for targeted therapy. To identify new and understudied mut-drivers, we developed a machine learning (ML) model that integrates curated clinical cancer data and posttranslational modification (PTM) proteomics databases. We applied the approach to 62,746 patient cancers spanning 84 cancer types and predicted 3,964 oncogenic mutations across 1,148 genes, many of which disrupt PTMs of known and unknown function. The list of putative mut-drivers includes established drivers and others with poorly understood roles in cancer. This ML model is available as a web application. As a case study, we focused the approach on nonreceptor tyrosine kinases (NRTK) and found a recurrent mutation in activated CDC42 kinase-1 (ACK1) that disrupts the Mig6 homology region (MHR) and ubiquitin-association (UBA) domains on the ACK1 C-terminus. By studying these domains in cultured cells, we found that disruption of the MHR domain helps activate the kinase while disruption of the UBA increases kinase stability by blocking its lysosomal degradation. This ACK1 mutation is analogous to lymphoma-associated mutations in its sister kinase, TNK1, which also disrupt a C-terminal inhibitory motif and UBA domain. This study establishes a mut-driver discovery tool for the research community and identifies a mechanism of ACK1 hyperactivation shared among ACK family kinases. IMPLICATIONS This research identifies a potentially targetable activating mutation in ACK1 and other possible oncogenic mutations, including PTM-disrupting mutations, for further study.
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Affiliation(s)
- Eranga R. Balasooriya
- The Fritz B. Burns Cancer Research Laboratory, Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah
- Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts
- Dept. of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Deshan Madhusanka
- The Fritz B. Burns Cancer Research Laboratory, Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah
- Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah
| | - Tania P. López-Palacios
- The Fritz B. Burns Cancer Research Laboratory, Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah
- Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah
| | - Riley J. Eastmond
- The Fritz B. Burns Cancer Research Laboratory, Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah
| | - Dasun Jayatunge
- The Fritz B. Burns Cancer Research Laboratory, Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah
- Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah
| | - Jake J. Owen
- The Fritz B. Burns Cancer Research Laboratory, Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah
| | - Jack S. Gashler
- The Fritz B. Burns Cancer Research Laboratory, Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah
| | - Christina M. Egbert
- The Fritz B. Burns Cancer Research Laboratory, Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah
| | | | - Lu Liu
- Department of Computer Science, North Dakota State University, Fargo, North Dakota
| | | | - Joshua L. Andersen
- The Fritz B. Burns Cancer Research Laboratory, Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah
- Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah
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2
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Harro CM, Sprenger KB, Chaurio RA, Powers JJ, Innamarato P, Anadon CM, Zhang Y, Biswas S, Mandal G, Mine JA, Cortina C, Nagy MZ, Martin AL, Handley KF, Borjas GJ, Chen PL, Pinilla-Ibarz J, Sokol L, Yu X, Conejo-Garcia JR. Sézary syndrome originates from heavily mutated hematopoietic progenitors. Blood Adv 2023; 7:5586-5602. [PMID: 37531660 PMCID: PMC10514084 DOI: 10.1182/bloodadvances.2022008562] [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: 07/14/2022] [Revised: 07/19/2023] [Accepted: 07/20/2023] [Indexed: 08/04/2023] Open
Abstract
The pathogenesis of cutaneous T-cell lymphoma (CTCL) remains unclear. Using single-cell RNA or T-cell receptor (TCR) sequencing of 32 619 CD3+CD4+ and CD26+/CD7+ and 29 932 CD3+CD4+ and CD26-/CD7- lymphocytes from the peripheral blood of 7 patients with CTCL, coupled to single-cell ATAC-sequencing of 26,411 CD3+CD4+ and CD26+/CD7+ and 33 841 CD3+CD4+ and CD26-/CD7- lymphocytes, we show that tumor cells in Sézary syndrome and mycosis fungoides (MF) exhibit different phenotypes and trajectories of differentiation. When compared to MF, Sézary cells exhibit narrower repertoires of TCRs and exhibit clonal enrichment. Surprisingly, we identified ≥200 mutations in hematopoietic stem cells from multiple patients with Sézary syndrome. Mutations in key oncogenes were also present in peripheral Sézary cells, which also showed the hallmarks of recent thymic egression. Together our data suggest that CTCL arises from mutated lymphocyte progenitors that acquire TCRs in the thymus, which complete their malignant transformation in the periphery.
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Affiliation(s)
- Carly M. Harro
- Department of Immunology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL
- Cancer Biology PhD Program, College of Arts and Sciences, University of South Florida, Tampa, FL
| | - Kimberly B. Sprenger
- Department of Immunology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL
| | - Ricardo A. Chaurio
- Department of Immunology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL
- Department of Immunology, Duke School of Medicine, Durham, NC
| | - John J. Powers
- Department of Immunology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL
| | - Patrick Innamarato
- Department of Immunology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL
| | - Carmen M. Anadon
- Department of Immunology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL
- Department of Immunology, Duke School of Medicine, Durham, NC
| | - Yumeng Zhang
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL
| | - Subir Biswas
- Department of Immunology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL
- Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, India
| | - Gunjan Mandal
- Department of Immunology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL
- Department of Biotechnology, Institute of Life Sciences, Bhubaneswar, India
| | - Jessica A. Mine
- Department of Immunology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL
- Department of Immunology, Duke School of Medicine, Durham, NC
| | - Carla Cortina
- Department of Immunology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL
| | - Mate Z. Nagy
- Department of Immunology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL
| | - Alexandra L. Martin
- Department of Gynecologic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL
| | - Katelyn F. Handley
- Department of Gynecologic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL
| | - Gustavo J. Borjas
- Department of Immunology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL
| | - Pei-Ling Chen
- Department of Pathology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL
| | - Javier Pinilla-Ibarz
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL
| | - Lubomir Sokol
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL
| | - Xiaoqing Yu
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL
| | - Jose R. Conejo-Garcia
- Department of Immunology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL
- Department of Immunology, Duke School of Medicine, Durham, NC
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL
- Department of Gynecologic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL
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3
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Kan Y, Paung Y, Seeliger MA, Miller WT. Domain Architecture of the Nonreceptor Tyrosine Kinase Ack1. Cells 2023; 12:900. [PMID: 36980241 PMCID: PMC10047419 DOI: 10.3390/cells12060900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/09/2023] [Accepted: 03/13/2023] [Indexed: 03/17/2023] Open
Abstract
The nonreceptor tyrosine kinase (NRTK) Ack1 comprises a distinct arrangement of non-catalytic modules. Its SH3 domain has a C-terminal to the kinase domain (SH1), in contrast to the typical SH3-SH2-SH1 layout in NRTKs. The Ack1 is the only protein that shares a region of high homology to the tumor suppressor protein Mig6, a modulator of EGFR. The vertebrate Acks make up the only tyrosine kinase (TK) family known to carry a UBA domain. The GTPase binding and SAM domains are also uncommon in the NRTKs. In addition to being a downstream effector of receptor tyrosine kinases (RTKs) and integrins, Ack1 can act as an epigenetic regulator, modulate the degradation of the epidermal growth factor receptor (EGFR), confer drug resistance, and mediate the progression of hormone-sensitive tumors. In this review, we discuss the domain architecture of Ack1 in relation to other protein kinases that possess such defined regulatory domains.
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Affiliation(s)
- Yagmur Kan
- Department of Physiology and Biophysics, School of Medicine, Stony Brook University, Stony Brook, NY 11794-8661, USA
| | - YiTing Paung
- Department of Pharmacology, School of Medicine, Stony Brook University, Stony Brook, NY 11794-8661, USA
| | - Markus A. Seeliger
- Department of Pharmacology, School of Medicine, Stony Brook University, Stony Brook, NY 11794-8661, USA
| | - W. Todd Miller
- Department of Physiology and Biophysics, School of Medicine, Stony Brook University, Stony Brook, NY 11794-8661, USA
- Department of Veterans Affairs Medical Center, Northport, NY 11768-2200, USA
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4
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Kan Y, Miller WT. Activity of the nonreceptor tyrosine kinase Ack1 is regulated by tyrosine phosphorylation of its Mig6 homology region. FEBS Lett 2022; 596:2808-2820. [PMID: 36178070 PMCID: PMC9879303 DOI: 10.1002/1873-3468.14505] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/19/2022] [Indexed: 01/28/2023]
Abstract
Ack1 is a proto-oncogenic tyrosine kinase with homology to the tumour suppressor Mig6, an inhibitor of the epidermal growth factor receptor (EGFR). The residues critical for binding of Mig6 to EGFR are conserved within the Mig6 homology region (MHR) of Ack1. We tested whether intramolecular interactions between the Ack1 MHR and kinase domain (KD) are regulated by phosphorylation. We identified two Src phosphorylation sites within the MHR (Y859, Y860). Addition of Src-phosphorylated MHR to the Ack1 KD enhanced enzymatic activity. Co-expression of Src in cells led to increased Ack1 activity; mutation of Y859/Y860 blocked this increase. Collectively, the data suggest that phosphorylation of the Ack1 MHR regulates its kinase activity. Phosphorylation of Y859/Y860 occurs in cancers of the brain, breast, colon, and prostate, where genomic amplification or somatic mutations of Ack1 play a role in disease progression. Our findings suggest that MHR phosphorylation could contribute to Ack1 dysregulation in tumours.
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Affiliation(s)
- Yağmur Kan
- Department of Physiology and Biophysics, School of Medicine Stony Brook University NY USA
| | - W. Todd Miller
- Department of Physiology and Biophysics, School of Medicine Stony Brook University NY USA
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5
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Arter C, Trask L, Ward S, Yeoh S, Bayliss R. Structural features of the protein kinase domain and targeted binding by small-molecule inhibitors. J Biol Chem 2022; 298:102247. [PMID: 35830914 PMCID: PMC9382423 DOI: 10.1016/j.jbc.2022.102247] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 07/04/2022] [Accepted: 07/06/2022] [Indexed: 12/17/2022] Open
Abstract
Protein kinases are key components in cellular signaling pathways as they carry out the phosphorylation of proteins, primarily on Ser, Thr, and Tyr residues. The catalytic activity of protein kinases is regulated, and they can be thought of as molecular switches that are controlled through protein-protein interactions and post-translational modifications. Protein kinases exhibit diverse structural mechanisms of regulation and have been fascinating subjects for structural biologists from the first crystal structure of a protein kinase over 30 years ago, to recent insights into kinase assemblies enabled by the breakthroughs in cryo-EM. Protein kinases are high-priority targets for drug discovery in oncology and other disease settings, and kinase inhibitors have transformed the outcomes of specific groups of patients. Most kinase inhibitors are ATP competitive, deriving potency by occupying the deep hydrophobic pocket at the heart of the kinase domain. Selectivity of inhibitors depends on exploiting differences between the amino acids that line the ATP site and exploring the surrounding pockets that are present in inactive states of the kinase. More recently, allosteric pockets outside the ATP site are being targeted to achieve high selectivity and to overcome resistance to current therapeutics. Here, we review the key regulatory features of the protein kinase family, describe the different types of kinase inhibitors, and highlight examples where the understanding of kinase regulatory mechanisms has gone hand in hand with the development of inhibitors.
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Affiliation(s)
- Chris Arter
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom; Faculty of Engineering and Physical Sciences, School of Chemistry, University of Leeds, Leeds, United Kingdom; Faculty of Biological Sciences, School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Luke Trask
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom; Faculty of Engineering and Physical Sciences, School of Chemistry, University of Leeds, Leeds, United Kingdom; Faculty of Biological Sciences, School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Sarah Ward
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom; Faculty of Engineering and Physical Sciences, School of Chemistry, University of Leeds, Leeds, United Kingdom
| | - Sharon Yeoh
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom; Faculty of Biological Sciences, School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Richard Bayliss
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom; Faculty of Biological Sciences, School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom.
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6
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Srivastava R. Chemical Reactivity and Optical and Pharmacokinetics Studies of 14 Multikinase Inhibitors and Their Docking Interactions Toward ACK1 for Precision Oncology. Front Chem 2022; 10:843642. [PMID: 35494626 PMCID: PMC9050413 DOI: 10.3389/fchem.2022.843642] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Accepted: 03/16/2022] [Indexed: 11/23/2022] Open
Abstract
Activated Cdc42-associated kinase 1 (ACK1/TNK2) has a significant role in cell endocytosis, survival, proliferation, and migration. Mutations in ACK1 are closely associated with the occurrence and development of cancers. In this work, a conceptual density functional theory (CDFT)-based computational peptidology (CDFT-CP) method is used to study the chemical reactivity of 14 multikinase inhibitors. Optical properties of these inhibitors are studied by time-dependent density functional theory (TDDFT). Various biological and pharmacokinetic parameters are studied by Osiris, Molinspiration, and BOILED-Egg in SwissADME software tools. Physicochemical and biopharmaceutical (PCB), Salmonella typhimurium reverse mutation assay (AMES) mutagenicity, toxicity, and risk prediction are estimated by Simulations plus ADMET Predictor 10.2 software. MD simulations for an active model of ACK1 is carried out by the CABS-flex 2.0 web server, and potential binding pockets for ACK1 are searched using the PrankWeb server. SwissTargetPrediction is used to predict the potential targets for the multikinase inhibitors. Docking studies are carried out for ACK1–multikinase inhibitors using Autodock 4.2 software. Noncovalent interactions for ACK1–multikinase inhibitor complexes are studied using the Protein–Ligand Interaction Profiler (PLIP) server. Results indicated higher binding affinities and strong noncovalent interactions in ACK1–multikinase inhibitor complexes.
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7
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Wang A, Pei J, Shuai W, Lin C, Feng L, Wang Y, Lin F, Ouyang L, Wang G. Small Molecules Targeting Activated Cdc42-Associated Kinase 1 (ACK1/TNK2) for the Treatment of Cancers. J Med Chem 2021; 64:16328-16348. [PMID: 34735773 DOI: 10.1021/acs.jmedchem.1c01030] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Activated Cdc42-associated kinase 1 (ACK1/TNK2) is a nonreceptor tyrosine kinase with a unique structure. It not only can act as an activated transmembrane effector of receptor tyrosine kinases (RTKs) to transmit various RTK signals but also can play a corresponding role in epigenetic regulation. A number of studies have shown that ACK1 is a carcinogenic factor. Blockage of ACK1 has been proven to be able to inhibit cancer cell survival, proliferation, migration, and radiation resistance. Thus, ACK1 is a promising potential antitumor target. To date, despite many efforts to develop ACK1 inhibitors, no specific small molecule inhibitors have entered clinical trials. This Perspective provides an overview of the structural features, biological functions, and association with diseases of ACK1 and in vitro and in vivo activities, selectivity, and therapeutic potential of small molecule ACK1 inhibitors with different chemotypes.
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Affiliation(s)
- Aoxue Wang
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Junping Pei
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Wen Shuai
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Congcong Lin
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Lu Feng
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Yuxi Wang
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Feng Lin
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China.,Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Liang Ouyang
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Guan Wang
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
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8
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TNK1 is a ubiquitin-binding and 14-3-3-regulated kinase that can be targeted to block tumor growth. Nat Commun 2021; 12:5337. [PMID: 34504101 PMCID: PMC8429728 DOI: 10.1038/s41467-021-25622-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 08/20/2021] [Indexed: 02/08/2023] Open
Abstract
TNK1 is a non-receptor tyrosine kinase with poorly understood biological function and regulation. Here, we identify TNK1 dependencies in primary human cancers. We also discover a MARK-mediated phosphorylation on TNK1 at S502 that promotes an interaction between TNK1 and 14-3-3, which sequesters TNK1 and inhibits its kinase activity. Conversely, the release of TNK1 from 14-3-3 allows TNK1 to cluster in ubiquitin-rich puncta and become active. Active TNK1 induces growth factor-independent proliferation of lymphoid cells in cell culture and mouse models. One unusual feature of TNK1 is a ubiquitin-association domain (UBA) on its C-terminus. Here, we characterize the TNK1 UBA, which has high affinity for poly-ubiquitin. Point mutations that disrupt ubiquitin binding inhibit TNK1 activity. These data suggest a mechanism in which TNK1 toggles between 14-3-3-bound (inactive) and ubiquitin-bound (active) states. Finally, we identify a TNK1 inhibitor, TP-5801, which shows nanomolar potency against TNK1-transformed cells and suppresses tumor growth in vivo.
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9
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Tahir R, Madugundu AK, Udainiya S, Cutler JA, Renuse S, Wang L, Pearson NA, Mitchell CJ, Mahajan N, Pandey A, Wu X. Proximity-Dependent Biotinylation to Elucidate the Interactome of TNK2 Nonreceptor Tyrosine Kinase. J Proteome Res 2021; 20:4566-4577. [PMID: 34428048 DOI: 10.1021/acs.jproteome.1c00551] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nonreceptor tyrosine kinases (NRTKs) represent an important class of signaling molecules driving diverse cellular pathways. Aberrant expression and hyperphosphorylation of TNK2, an NRTK, have been implicated in multiple cancers. However, the exact proteins and cellular events that mediate phenotypic changes downstream of TNK2 are unclear. Biological systems that employ proximity-dependent biotinylation methods, such as BioID, are being increasingly used to map protein-protein interactions, as they provide increased sensitivity in discovering interaction partners. In this study, we employed stable isotope labeling with amino acids in cell culture and BioID coupled to the biotinylation site identification technology (BioSITe) method that we recently developed to quantitatively explore the interactome of TNK2. By performing a controlled comparative analysis between full-length TNK2 and its truncated counterpart, we were able to not only identify site-level biotinylation of previously well-established TNK2 binders and substrates including NCK1, NCK2, CTTN, and STAT3, but also discover several novel TNK2 interacting partners. We also performed co-immunoprecipitation and immunofluorescence analysis to validate the interaction between TNK2 and CLINT1, a novel TNK2 interacting protein. Overall, this work reveals the power of the BioSITe method coupled to BioID and highlights several molecules that warrant further exploration to assess their functional significance in TNK2-mediated signaling.
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Affiliation(s)
- Raiha Tahir
- Biochemistry, Cellular and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States.,Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States.,Ginkgo Bioworks, Boston, Massachusetts 02210, United States
| | - Anil K Madugundu
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States.,Institute of Bioinformatics, International Technology Park, Bangalore 560066, Karnataka, India.,Manipal Academy of Higher Education (MAHE), Manipal 576104, Karnataka, India.,Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Hosur Road, Bangalore 560029, Karnataka, India.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, United States
| | - Savita Udainiya
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States.,Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Hosur Road, Bangalore 560029, Karnataka, India.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, United States
| | - Jevon A Cutler
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States.,Pre-Doctoral Training Program in Human Genetics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Santosh Renuse
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, United States.,Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, United States
| | - Li Wang
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, United States
| | - Nicole A Pearson
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, United States
| | | | - Nupam Mahajan
- Siteman Cancer Center, Washington University, St. Louis, Missouri 63110, United States
| | - Akhilesh Pandey
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States.,Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Hosur Road, Bangalore 560029, Karnataka, India.,Departments of Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, United States.,Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, United States
| | - Xinyan Wu
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, United States.,Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota 55905, United States
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10
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Kumar V, Kumar R, Parate S, Yoon S, Lee G, Kim D, Lee KW. Identification of ACK1 inhibitors as anticancer agents by using computer-aided drug designing. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130200] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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11
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Li Z, Powell CE, Groendyke BJ, Gero TW, Feru F, Feutrill J, Chen B, Li B, Szabo H, Gray NS, Scott DA. Discovery of a series of benzopyrimidodiazepinone TNK2 inhibitors via scaffold morphing. Bioorg Med Chem Lett 2020; 30:127456. [PMID: 32739400 DOI: 10.1016/j.bmcl.2020.127456] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/23/2020] [Accepted: 07/24/2020] [Indexed: 11/30/2022]
Abstract
The protein kinase TNK2 (ACK1) is an emerging drug target for a variety of indications, in particular for cancer where it plays a key role transmitting cell survival, growth and proliferative signals via modification of multiple downstream effectors by unique tyrosine phosphorylation events. Scaffold morphing based on our previous TNK2 inhibitor XMD8-87 identified urea 17 from which we developed the potent and selective compound 32. A co-crystal structure was obtained showing 32 interacting primarily with the main chain atoms of an alanine residue of the hinge region. Additional H-bonds exist between the urea NHs and the Thr205 and Asp270 residues.
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Affiliation(s)
- Zhengnian Li
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, 360 Longwood Ave, Boston, MA 02115, USA
| | - Chelsea E Powell
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, 360 Longwood Ave, Boston, MA 02115, USA
| | - Brian J Groendyke
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, 360 Longwood Ave, Boston, MA 02115, USA
| | - Thomas W Gero
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, 360 Longwood Ave, Boston, MA 02115, USA
| | - Frederic Feru
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, 360 Longwood Ave, Boston, MA 02115, USA
| | - John Feutrill
- SYNthesis med chem, 425 Changyang Street, Suzhou Industry Park, Suzhou, Jiangsu, China
| | - Bailing Chen
- SYNthesis med chem, 425 Changyang Street, Suzhou Industry Park, Suzhou, Jiangsu, China
| | - Bin Li
- SYNthesis med chem, 425 Changyang Street, Suzhou Industry Park, Suzhou, Jiangsu, China
| | - Hilary Szabo
- Vivid BioSciences, 50 Northern Ave, Boston, MA 02210, USA
| | - Nathanael S Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, 360 Longwood Ave, Boston, MA 02115, USA.
| | - David A Scott
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, 360 Longwood Ave, Boston, MA 02115, USA.
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12
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Kim EH, Cao D, Mahajan NP, Andriole GL, Mahajan K. ACK1-AR and AR-HOXB13 signaling axes: epigenetic regulation of lethal prostate cancers. NAR Cancer 2020; 2:zcaa018. [PMID: 32885168 PMCID: PMC7454006 DOI: 10.1093/narcan/zcaa018] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 07/22/2020] [Accepted: 08/13/2020] [Indexed: 12/24/2022] Open
Abstract
The androgen receptor (AR) is a critical transcription factor in prostate cancer (PC) pathogenesis. Its activity in malignant cells is dependent on interactions with a diverse set of co-regulators. These interactions fluctuate depending on androgen availability. For example, the androgen depletion increases the dependence of castration-resistant PCs (CRPCs) on the ACK1 and HOXB13 cell survival pathways. Activated ACK1, an oncogenic tyrosine kinase, phosphorylates cytosolic and nuclear proteins, thereby avoiding the inhibitory growth consequences of androgen depletion. Notably, ACK1-mediated phosphorylation of histone H4, which leads to epigenetic upregulation of AR expression, has emerged as a critical mechanism of CRPC resistance to anti-androgens. This resistance can be targeted using the ACK1-selective small-molecule kinase inhibitor (R)- 9b. CRPCs also deploy the bromodomain and extra-terminal domain protein BRD4 to epigenetically increase HOXB13 gene expression, which in turn activates the MYC target genes AURKA/AURKB. HOXB13 also facilitates ligand-independent recruitment of the AR splice variant AR-V7 to chromatin, compensating for the loss of the chromatin remodeling protein, CHD1, and restricting expression of the mitosis control gene HSPB8. These studies highlight the crosstalk between AR-ACK1 and AR-HOXB13 pathways as key mediators of CRPC recurrence.
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Affiliation(s)
- Eric H Kim
- Division of Urologic Surgery, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Dengfeng Cao
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Nupam P Mahajan
- Division of Urologic Surgery, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Gerald L Andriole
- Division of Urologic Surgery, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Kiran Mahajan
- Division of Urologic Surgery, Washington University in St. Louis, St. Louis, MO 63110, USA
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13
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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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14
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Ferguson FM, Liu Y, Harshbarger W, Huang L, Wang J, Deng X, Capuzzi SJ, Muratov EN, Tropsha A, Muthuswamy S, Westover KD, Gray NS. Synthesis and Structure-Activity Relationships of DCLK1 Kinase Inhibitors Based on a 5,11-Dihydro-6 H-benzo[ e]pyrimido[5,4- b][1,4]diazepin-6-one Scaffold. J Med Chem 2020; 63:7817-7826. [PMID: 32530623 DOI: 10.1021/acs.jmedchem.0c00596] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Doublecortin-like kinase 1 (DCLK1) is a serine/threonine kinase that is overexpressed in gastrointestinal cancers, including esophageal, gastric, colorectal, and pancreatic cancers. DCLK1 is also used as a marker of tuft cells, which regulate type II immunity in the gut. However, the substrates and functions of DCLK1 are understudied. We recently described the first selective DCLK1/2 inhibitor, DCLK1-IN-1, developed to aid the functional characterization of this important kinase. Here we describe the synthesis and structure-activity relationships of 5,11-dihydro-6H-benzo[e]pyrimido[5,4-b][1,4]diazepin-6-one DCLK1 inhibitors, resulting in the identification of DCLK1-IN-1.
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Affiliation(s)
- Fleur M Ferguson
- Department of Cancer Biology, Dana-Farber Cancer Institute, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Yan Liu
- Departments of Radiation Oncology and Biochemistry, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390, United States
| | - Wayne Harshbarger
- Departments of Radiation Oncology and Biochemistry, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390, United States
| | - Ling Huang
- Cancer Research Institute and Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Jinhua Wang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Xianming Deng
- Department of Cancer Biology, Dana-Farber Cancer Institute, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Stephen J Capuzzi
- UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Eugene N Muratov
- UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Alexander Tropsha
- UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Senthil Muthuswamy
- Cancer Research Institute and Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, United States.,Departments of Medicine and Pathology, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Kenneth D Westover
- Departments of Radiation Oncology and Biochemistry, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390, United States
| | - Nathanael S Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
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15
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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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16
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Groendyke BJ, Powell CE, Feru F, Gero TW, Li Z, Szabo H, Pang K, Feutrill J, Chen B, Li B, Gray NS, Scott DA. Benzopyrimidodiazepinone inhibitors of TNK2. Bioorg Med Chem Lett 2020; 30:126948. [PMID: 31928839 DOI: 10.1016/j.bmcl.2020.126948] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 12/20/2019] [Accepted: 01/01/2020] [Indexed: 11/30/2022]
Abstract
The SAR of a series of benzopyrimidodiazepinone inhibitors of TNK2 was developed, starting from the potent and selective compound XMD8-87. A diverse set of anilines was introduced in an effort to improve the in vivo PK profile and minimize the risk of quinone diimine formation.
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Affiliation(s)
- Brian J Groendyke
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, 360 Longwood Ave, Boston, MA 02115, USA
| | - Chelsea E Powell
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, 360 Longwood Ave, Boston, MA 02115, USA
| | - Frederic Feru
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, 360 Longwood Ave, Boston, MA 02115, USA
| | - Thomas W Gero
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, 360 Longwood Ave, Boston, MA 02115, USA
| | - Zhengnian Li
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, 360 Longwood Ave, Boston, MA 02115, USA
| | - Hilary Szabo
- Vivid BioSciences, 50 Northern Ave, Boston, MA 02210, USA
| | - Kevin Pang
- Northeastern University, 360 Huntington Ave, Boston, MA 02115, USA
| | - John Feutrill
- SYNthesis Med Chem, 425 Changyang Street, Suzhou Industry Park, Suzhou, Jiangsu, China
| | - Bailing Chen
- SYNthesis Med Chem, 425 Changyang Street, Suzhou Industry Park, Suzhou, Jiangsu, China
| | - Bin Li
- SYNthesis Med Chem, 425 Changyang Street, Suzhou Industry Park, Suzhou, Jiangsu, China
| | - Nathanael S Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, 360 Longwood Ave, Boston, MA 02115, USA
| | - David A Scott
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, 360 Longwood Ave, Boston, MA 02115, USA
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17
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Research Progress of the Functional Role of ACK1 in Breast Cancer. BIOMED RESEARCH INTERNATIONAL 2019; 2019:1018034. [PMID: 31772931 PMCID: PMC6854235 DOI: 10.1155/2019/1018034] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 09/13/2019] [Indexed: 01/25/2023]
Abstract
ACK1 is a nonreceptor tyrosine kinase with a unique structure, which is tightly related to the biological behavior of tumors. Previous studies have demonstrated that ACK1 was involved with multiple signaling pathways of tumor progression. Its crucial role in tumor cell proliferation, apoptosis, invasion, and metastasis was tightly related to the prognosis and clinicopathology of cancer. ACK1 has a unique way of regulating cellular pathways, different from other nonreceptor tyrosine kinases. As an oncogenic kinase, recent studies have shown that ACK1 plays a critical regulatory role in the initiation and progression of tumors. In this review, we will be summarizing the structural characteristics, activation, and regulation of ACK1 in breast cancer, aiming to deeply understand the functional and mechanistic role of ACK1 and provide novel therapeutic strategies for breast cancer treatment.
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18
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Jenkins C, Luty SB, Maxson JE, Eide CA, Abel ML, Togiai C, Nemecek ER, Bottomly D, McWeeney SK, Wilmot B, Loriaux M, Chang BH, Tyner JW. Synthetic lethality of TNK2 inhibition in PTPN11-mutant leukemia. Sci Signal 2018; 11:eaao5617. [PMID: 30018082 PMCID: PMC6168748 DOI: 10.1126/scisignal.aao5617] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The protein tyrosine phosphatase PTPN11 is implicated in the pathogenesis of juvenile myelomonocytic leukemia (JMML), acute myeloid leukemia (AML), and other malignancies. Activating mutations in PTPN11 increase downstream proliferative signaling and cell survival. We investigated the signaling upstream of PTPN11 in JMML and AML cells and found that PTPN11 was activated by the nonreceptor tyrosine/serine/threonine kinase TNK2 and that PTPN11-mutant JMML and AML cells were sensitive to TNK2 inhibition. In cultured human cell-based assays, PTPN11 and TNK2 interacted directly, enabling TNK2 to phosphorylate PTPN11, which subsequently dephosphorylated TNK2 in a negative feedback loop. Mutations in PTPN11 did not affect this physical interaction but increased the basal activity of PTPN11 such that TNK2-mediated activation was additive. Consequently, coexpression of TNK2 and mutant PTPN11 synergistically increased mitogen-activated protein kinase (MAPK) signaling and enhanced colony formation in bone marrow cells from mice. Chemical inhibition of TNK2 blocked MAPK signaling and colony formation in vitro and decreased disease burden in a patient with PTPN11-mutant JMML who was treated with the multikinase (including TNK2) inhibitor dasatinib. Together, these data suggest that TNK2 is a promising therapeutic target for PTPN11-mutant leukemias.
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MESH Headings
- Animals
- Child
- Dasatinib/pharmacology
- Humans
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/enzymology
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/pathology
- Leukemia, Myelomonocytic, Juvenile/drug therapy
- Leukemia, Myelomonocytic, Juvenile/enzymology
- Leukemia, Myelomonocytic, Juvenile/genetics
- Leukemia, Myelomonocytic, Juvenile/pathology
- Male
- Mice
- Prognosis
- Protein Kinase Inhibitors/pharmacology
- Protein Tyrosine Phosphatase, Non-Receptor Type 11/genetics
- Protein-Tyrosine Kinases/antagonists & inhibitors
- Signal Transduction
- Survival Rate
- Synthetic Lethal Mutations
- Tumor Stem Cell Assay
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Affiliation(s)
- Chelsea Jenkins
- Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, Portland, OR 97239, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Samuel B Luty
- Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, Portland, OR 97239, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Julia E Maxson
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Division of Hematology and Medical Oncology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Christopher A Eide
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Melissa L Abel
- Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, Portland, OR 97239, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Corinne Togiai
- Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, Portland, OR 97239, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Eneida R Nemecek
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Pediatrics, Oregon Health & Science University, Portland, OR 97239, USA
| | - Daniel Bottomly
- Oregon Clinical and Translational Research Institute, Portland, OR 97239, USA
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Shannon K McWeeney
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Oregon Clinical and Translational Research Institute, Portland, OR 97239, USA
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Beth Wilmot
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Oregon Clinical and Translational Research Institute, Portland, OR 97239, USA
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Marc Loriaux
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Pathology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Bill H Chang
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA.
- Department of Pediatrics, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jeffrey W Tyner
- Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, Portland, OR 97239, USA.
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
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19
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He S, Tong X, Han M, Bai Y, Dai F. Genome-Wide Identification and Characterization of Tyrosine Kinases in the Silkworm, Bombyx mori. Int J Mol Sci 2018; 19:E934. [PMID: 29561793 PMCID: PMC5979338 DOI: 10.3390/ijms19040934] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 03/16/2018] [Accepted: 03/20/2018] [Indexed: 12/19/2022] Open
Abstract
The tyrosine kinases (TKs) are important parts of metazoan signaling pathways and play significant roles in cell growth, development, apoptosis and disease. Genome-wide characterization of TKs has been conducted in many metazoans, however, systematic information about this family in Lepidoptera is still lacking. We retrieved 33 TK-encoding genes in silkworm and classified them into 25 subfamilies by sequence analysis, without members in AXL, FRK, PDGFR, STYK1 and TIE subfamilies. Although domain sequences in each subfamily are conserved, TKs in vertebrates tend to be remarkably conserved and stable. Our results of phylogenetic analysis supported the previous conclusion for the second major expansion of TK family. Gene-Ontology (GO) analysis revealed that a higher proportion of BmTKs played roles in binding, catalysis, signal transduction, metabolism, biological regulation and response to stimulus, compared to all silkworm genes annotated in GO. Moreover, the expression profile analysis of BmTKs among multiple tissues and developmental stages demonstrated that many genes exhibited stage-specific and/or sex-related expression during embryogenesis, molting and metamorphosis, and that 8 BmTKs presented tissue-specific high expression. Our study provides systematic description of silkworm tyrosine kinases, and may also provide further insights into metazoan TKs and assist future studies addressing their functions.
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Affiliation(s)
- Songzhen He
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing 400715, China.
| | - Xiaoling Tong
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing 400715, China.
| | - Minjin Han
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing 400715, China.
| | - Yanmin Bai
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing 400715, China.
| | - Fangyin Dai
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing 400715, China.
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20
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Lai Y, Zhao Z, Zeng T, Liang X, Chen D, Duan X, Zeng G, Wu W. Crosstalk between VEGFR and other receptor tyrosine kinases for TKI therapy of metastatic renal cell carcinoma. Cancer Cell Int 2018. [PMID: 29527128 PMCID: PMC5838927 DOI: 10.1186/s12935-018-0530-2] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is the most common subtype of renal cell carcinoma (RCC), and is frequently accompanied by the genetic features of von Hippel–Lindau (VHL) loss. VHL loss increases the expression of hypoxia-inducible factors (HIFs) and their targets, including epidermal growth factor (EGF), vascular endothelial growth factor (VEGF), and platelet-derived growth factor (PDGF). The primary treatment for metastatic RCC (mRCC) is molecular-targeted therapy, especially anti-angiogenic therapy. VEGF monoclonal antibodies and VEGF receptor (VEGFR) tyrosine kinase inhibitors (TKIs) are the main drugs used in anti-angiogenic therapy. However, crosstalk between VEGFR and other tyrosine kinase or downstream pathways produce resistance to TKI treatment, and the multi-target inhibitors, HIF inhibitors or combination strategies are promising strategies for mRCC. HIFs are upstream of the crosstalk between the growth factors, and these factors may regulate the expression of VEGR, EGF, PDGF and other growth factors. The frequent VHL loss in ccRCC increases HIF expression, and HIFs may be an ideal candidate to overcome the TKI resistance. The combination of HIF inhibitors and immune checkpoint inhibitors is also anticipated. Various clinical trials of programmed cell death protein 1 inhibitors are planned. The present study reviews the effects of current and potential TKIs on mRCC, with a focus on VEGF/VEGFR and other targets for mRCC therapy.
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Affiliation(s)
- Yongchang Lai
- Department of Urology, Minimally Invasive Surgery Center, Guangzhou Urology Research Institute, Guangdong Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Kangda Road 1#, Haizhu District, Guangzhou, 510230 Guangdong China
| | - Zhijian Zhao
- Department of Urology, Minimally Invasive Surgery Center, Guangzhou Urology Research Institute, Guangdong Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Kangda Road 1#, Haizhu District, Guangzhou, 510230 Guangdong China
| | - Tao Zeng
- Department of Urology, Minimally Invasive Surgery Center, Guangzhou Urology Research Institute, Guangdong Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Kangda Road 1#, Haizhu District, Guangzhou, 510230 Guangdong China
| | - Xiongfa Liang
- Department of Urology, Minimally Invasive Surgery Center, Guangzhou Urology Research Institute, Guangdong Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Kangda Road 1#, Haizhu District, Guangzhou, 510230 Guangdong China
| | - Dong Chen
- Department of Urology, Minimally Invasive Surgery Center, Guangzhou Urology Research Institute, Guangdong Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Kangda Road 1#, Haizhu District, Guangzhou, 510230 Guangdong China
| | - Xiaolu Duan
- Department of Urology, Minimally Invasive Surgery Center, Guangzhou Urology Research Institute, Guangdong Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Kangda Road 1#, Haizhu District, Guangzhou, 510230 Guangdong China
| | - Guohua Zeng
- Department of Urology, Minimally Invasive Surgery Center, Guangzhou Urology Research Institute, Guangdong Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Kangda Road 1#, Haizhu District, Guangzhou, 510230 Guangdong China
| | - Wenqi Wu
- Department of Urology, Minimally Invasive Surgery Center, Guangzhou Urology Research Institute, Guangdong Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Kangda Road 1#, Haizhu District, Guangzhou, 510230 Guangdong China
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21
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Siveen KS, Prabhu KS, Achkar IW, Kuttikrishnan S, Shyam S, Khan AQ, Merhi M, Dermime S, Uddin S. Role of Non Receptor Tyrosine Kinases in Hematological Malignances and its Targeting by Natural Products. Mol Cancer 2018; 17:31. [PMID: 29455667 PMCID: PMC5817858 DOI: 10.1186/s12943-018-0788-y] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 02/01/2018] [Indexed: 12/12/2022] Open
Abstract
Tyrosine kinases belong to a family of enzymes that mediate the movement of the phosphate group to tyrosine residues of target protein, thus transmitting signals from the cell surface to cytoplasmic proteins and the nucleus to regulate physiological processes. Non-receptor tyrosine kinases (NRTK) are a sub-group of tyrosine kinases, which can relay intracellular signals originating from extracellular receptor. NRTKs can regulate a huge array of cellular functions such as cell survival, division/propagation and adhesion, gene expression, immune response, etc. NRTKs exhibit considerable variability in their structural make up, having a shared kinase domain and commonly possessing many other domains such as SH2, SH3 which are protein-protein interacting domains. Recent studies show that NRTKs are mutated in several hematological malignancies, including lymphomas, leukemias and myelomas, leading to aberrant activation. It can be due to point mutations which are intragenic changes or by fusion of genes leading to chromosome translocation. Mutations that lead to constitutive kinase activity result in the formation of oncogenes, such as Abl, Fes, Src, etc. Therefore, specific kinase inhibitors have been sought after to target mutated kinases. A number of compounds have since been discovered, which have shown to inhibit the activity of NRTKs, which are remarkably well tolerated. This review covers the role of various NRTKs in the development of hematological cancers, including their deregulation, genetic alterations, aberrant activation and associated mutations. In addition, it also looks at the recent advances in the development of novel natural compounds that can target NRTKs and perhaps in combination with other forms of therapy can show great promise for the treatment of hematological malignancies.
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Affiliation(s)
- Kodappully S Siveen
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, PO Box 3050, Doha, State of Qatar
| | - Kirti S Prabhu
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, PO Box 3050, Doha, State of Qatar
| | - Iman W Achkar
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, PO Box 3050, Doha, State of Qatar
| | - Shilpa Kuttikrishnan
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, PO Box 3050, Doha, State of Qatar
| | - Sunitha Shyam
- Medical Research Center, Hamad Medical Corporation, Doha, State of Qatar
| | - Abdul Q Khan
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, PO Box 3050, Doha, State of Qatar
| | - Maysaloun Merhi
- Translational Cancer Research Facility, National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, State of Qatar
| | - Said Dermime
- Translational Cancer Research Facility, National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, State of Qatar
| | - Shahab Uddin
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, PO Box 3050, Doha, State of Qatar.
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22
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Dietrich S, Oleś M, Lu J, Sellner L, Anders S, Velten B, Wu B, Hüllein J, da Silva Liberio M, Walther T, Wagner L, Rabe S, Ghidelli-Disse S, Bantscheff M, Oleś AK, Słabicki M, Mock A, Oakes CC, Wang S, Oppermann S, Lukas M, Kim V, Sill M, Benner A, Jauch A, Sutton LA, Young E, Rosenquist R, Liu X, Jethwa A, Lee KS, Lewis J, Putzker K, Lutz C, Rossi D, Mokhir A, Oellerich T, Zirlik K, Herling M, Nguyen-Khac F, Plass C, Andersson E, Mustjoki S, von Kalle C, Ho AD, Hensel M, Dürig J, Ringshausen I, Zapatka M, Huber W, Zenz T. Drug-perturbation-based stratification of blood cancer. J Clin Invest 2018; 128:427-445. [PMID: 29227286 PMCID: PMC5749541 DOI: 10.1172/jci93801] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 10/31/2017] [Indexed: 12/11/2022] Open
Abstract
As new generations of targeted therapies emerge and tumor genome sequencing discovers increasingly comprehensive mutation repertoires, the functional relationships of mutations to tumor phenotypes remain largely unknown. Here, we measured ex vivo sensitivity of 246 blood cancers to 63 drugs alongside genome, transcriptome, and DNA methylome analysis to understand determinants of drug response. We assembled a primary blood cancer cell encyclopedia data set that revealed disease-specific sensitivities for each cancer. Within chronic lymphocytic leukemia (CLL), responses to 62% of drugs were associated with 2 or more mutations, and linked the B cell receptor (BCR) pathway to trisomy 12, an important driver of CLL. Based on drug responses, the disease could be organized into phenotypic subgroups characterized by exploitable dependencies on BCR, mTOR, or MEK signaling and associated with mutations, gene expression, and DNA methylation. Fourteen percent of CLLs were driven by mTOR signaling in a non-BCR-dependent manner. Multivariate modeling revealed immunoglobulin heavy chain variable gene (IGHV) mutation status and trisomy 12 as the most important modulators of response to kinase inhibitors in CLL. Ex vivo drug responses were associated with outcome. This study overcomes the perception that most mutations do not influence drug response of cancer, and points to an updated approach to understanding tumor biology, with implications for biomarker discovery and cancer care.
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MESH Headings
- Antineoplastic Agents/therapeutic use
- Chromosomes, Human, Pair 12/genetics
- Chromosomes, Human, Pair 12/metabolism
- Databases, Factual
- Female
- Hematologic Neoplasms/classification
- Hematologic Neoplasms/drug therapy
- Hematologic Neoplasms/genetics
- Hematologic Neoplasms/pathology
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/classification
- Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Male
- Models, Biological
- Neoplasm Proteins/genetics
- Neoplasm Proteins/metabolism
- Signal Transduction
- Trisomy/genetics
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Affiliation(s)
- Sascha Dietrich
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Department of Medicine V, University Hospital Heidelberg, Heidelberg, Germany
- Molecular Therapy in Hematology and Oncology, and Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Centre, Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
| | - Małgorzata Oleś
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Junyan Lu
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Leopold Sellner
- Department of Medicine V, University Hospital Heidelberg, Heidelberg, Germany
- Molecular Therapy in Hematology and Oncology, and Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Centre, Heidelberg, Germany
| | - Simon Anders
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Britta Velten
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Bian Wu
- Molecular Therapy in Hematology and Oncology, and Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Centre, Heidelberg, Germany
| | - Jennifer Hüllein
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Molecular Therapy in Hematology and Oncology, and Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Centre, Heidelberg, Germany
| | - Michelle da Silva Liberio
- Molecular Therapy in Hematology and Oncology, and Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Centre, Heidelberg, Germany
| | - Tatjana Walther
- Molecular Therapy in Hematology and Oncology, and Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Centre, Heidelberg, Germany
| | - Lena Wagner
- Molecular Therapy in Hematology and Oncology, and Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Centre, Heidelberg, Germany
| | - Sophie Rabe
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Department of Medicine V, University Hospital Heidelberg, Heidelberg, Germany
- Molecular Therapy in Hematology and Oncology, and Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Centre, Heidelberg, Germany
| | | | | | - Andrzej K. Oleś
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Mikołaj Słabicki
- Molecular Therapy in Hematology and Oncology, and Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Centre, Heidelberg, Germany
| | - Andreas Mock
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Christopher C. Oakes
- Division of Hematology, Departments of Internal Medicine and Biomedical Informatics, The Ohio State University, Columbus, Ohio, USA
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Centre, Heidelberg, Germany
| | - Shihui Wang
- Molecular Therapy in Hematology and Oncology, and Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Centre, Heidelberg, Germany
| | - Sina Oppermann
- Molecular Therapy in Hematology and Oncology, and Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Centre, Heidelberg, Germany
| | - Marina Lukas
- Molecular Therapy in Hematology and Oncology, and Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Centre, Heidelberg, Germany
| | - Vladislav Kim
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Martin Sill
- Division of Biostatistics, German Cancer Research Centre, Heidelberg, Germany
| | - Axel Benner
- Division of Biostatistics, German Cancer Research Centre, Heidelberg, Germany
| | - Anna Jauch
- Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany
| | - Lesley Ann Sutton
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Emma Young
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Xiyang Liu
- Molecular Therapy in Hematology and Oncology, and Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Centre, Heidelberg, Germany
| | - Alexander Jethwa
- Molecular Therapy in Hematology and Oncology, and Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Centre, Heidelberg, Germany
| | - Kwang Seok Lee
- Molecular Therapy in Hematology and Oncology, and Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Centre, Heidelberg, Germany
| | - Joe Lewis
- European Molecular Biology Laboratory (EMBL), Chemical Biology Core Facility, Heidelberg, Germany
| | - Kerstin Putzker
- European Molecular Biology Laboratory (EMBL), Chemical Biology Core Facility, Heidelberg, Germany
| | - Christoph Lutz
- Department of Medicine V, University Hospital Heidelberg, Heidelberg, Germany
| | - Davide Rossi
- Department of Translational Medicine, Amedeo Avogadro University of Eastern Piedmont, Novara, Italy; Division of Hematology, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Andriy Mokhir
- Friedrich-Alexander-University of Erlangen-Nürnberg, Department of Chemistry and Pharmacy, Organic Chemistry II, Erlangen, Germany
| | - Thomas Oellerich
- Hematology/Oncology, Department of Medicine, Johann Wolfgang Goethe University, Frankfurt, Germany; Department of Haematology, Cambridge Institute of Medical Research, University of Cambridge, Cambridge, United Kingdom
- German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Katja Zirlik
- German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
- Department of Hematology/Oncology, University Hospital Freiburg, Freiburg, Germany and Tumorzentrum ZeTuP Chur, Chur, Schweiz
| | - Marco Herling
- Department of Internal Medicine I, University Hospital Cologne, Cologne, Germany
| | - Florence Nguyen-Khac
- INSERM U1138, Université Pierre et Marie Curie-Paris and Service d’Hématologie Biologique, Hôpital Pitié-Salpêtrière, Paris, France
| | - Christoph Plass
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Centre, Heidelberg, Germany
- German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Emma Andersson
- Hematology Research Unit Helsinki, University of Helsinki, Helsinki, Finland and Department of Hematology, Comprehensive Cancer Centre, Helsinki University Hospital, Helsinki, Finland
| | - Satu Mustjoki
- Hematology Research Unit Helsinki, University of Helsinki, Helsinki, Finland and Department of Hematology, Comprehensive Cancer Centre, Helsinki University Hospital, Helsinki, Finland
| | - Christof von Kalle
- Molecular Therapy in Hematology and Oncology, and Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Centre, Heidelberg, Germany
- German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
- Heidelberg Centre for Personalized Oncology, DKFZ-HIPO, DKFZ, Heidelberg, Germany
| | - Anthony D. Ho
- Department of Medicine V, University Hospital Heidelberg, Heidelberg, Germany
| | | | - Jan Dürig
- German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
- Department of Hematology, University Hospital Essen, Essen, Germany
| | - Ingo Ringshausen
- Department of Hematology, University of Cambridge, Cambridge, United Kingdom
| | - Marc Zapatka
- Division of Molecular Genetics, German Cancer Research Centre, Heidelberg, Germany
| | - Wolfgang Huber
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
| | - Thorsten Zenz
- Department of Medicine V, University Hospital Heidelberg, Heidelberg, Germany
- Molecular Therapy in Hematology and Oncology, and Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Centre, Heidelberg, Germany
- German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
- Department of Hematology, University of Zürich, Zürich, Switzerland
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23
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Lue HW, Podolak J, Kolahi K, Cheng L, Rao S, Garg D, Xue CH, Rantala JK, Tyner JW, Thornburg KL, Martinez-Acevedo A, Liu JJ, Amling CL, Truillet C, Louie SM, Anderson KE, Evans MJ, O'Donnell VB, Nomura DK, Drake JM, Ritz A, Thomas GV. Metabolic reprogramming ensures cancer cell survival despite oncogenic signaling blockade. Genes Dev 2017; 31:2067-2084. [PMID: 29138276 PMCID: PMC5733498 DOI: 10.1101/gad.305292.117] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 10/26/2017] [Indexed: 12/19/2022]
Abstract
Lue et al. show that although inhibition of PI3K–AKT–mTOR signaling markedly decreased glycolysis and restrained tumor growth, these signaling and metabolic restrictions triggered autophagy. Survival of cancer cells was critically dependent on phospholipase A2 (PLA2) to mobilize lysophospholipids and free fatty acids to sustain fatty acid oxidation and oxidative phosphorylation. There is limited knowledge about the metabolic reprogramming induced by cancer therapies and how this contributes to therapeutic resistance. Here we show that although inhibition of PI3K–AKT–mTOR signaling markedly decreased glycolysis and restrained tumor growth, these signaling and metabolic restrictions triggered autophagy, which supplied the metabolites required for the maintenance of mitochondrial respiration and redox homeostasis. Specifically, we found that survival of cancer cells was critically dependent on phospholipase A2 (PLA2) to mobilize lysophospholipids and free fatty acids to sustain fatty acid oxidation and oxidative phosphorylation. Consistent with this, we observed significantly increased lipid droplets, with subsequent mobilization to mitochondria. These changes were abrogated in cells deficient for the essential autophagy gene ATG5. Accordingly, inhibition of PLA2 significantly decreased lipid droplets, decreased oxidative phosphorylation, and increased apoptosis. Together, these results describe how treatment-induced autophagy provides nutrients for cancer cell survival and identifies novel cotreatment strategies to override this survival advantage.
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Affiliation(s)
- Hui-Wen Lue
- Knight Comprehensive Cancer Institute, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Jennifer Podolak
- Knight Comprehensive Cancer Institute, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Kevin Kolahi
- Knight Cardiovascular Institute, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Larry Cheng
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08903, USA
| | - Soumya Rao
- Knight Comprehensive Cancer Institute, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Devin Garg
- Knight Comprehensive Cancer Institute, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Chang-Hui Xue
- Knight Comprehensive Cancer Institute, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Juha K Rantala
- Knight Comprehensive Cancer Institute, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Jeffrey W Tyner
- Knight Comprehensive Cancer Institute, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Kent L Thornburg
- Knight Cardiovascular Institute, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Ann Martinez-Acevedo
- Department of Urology, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Jen-Jane Liu
- Department of Urology, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Christopher L Amling
- Department of Urology, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Charles Truillet
- Department of Radiology, University of California at San Francisco School of Medicine, San Francisco, California 94107, USA
| | - Sharon M Louie
- University of California at Berkeley, Berkeley, California 94720, USA
| | | | - Michael J Evans
- Department of Radiology, University of California at San Francisco School of Medicine, San Francisco, California 94107, USA
| | - Valerie B O'Donnell
- Systems Immunity Research Institute, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - Daniel K Nomura
- University of California at Berkeley, Berkeley, California 94720, USA
| | - Justin M Drake
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08903, USA
| | - Anna Ritz
- Department of Biology, Reed College, Portland, Oregon 97202, USA
| | - George V Thomas
- Knight Comprehensive Cancer Institute, Oregon Health and Science University, Portland, Oregon 97239, USA.,Department of Pathology and Laboratory Medicine, Oregon Health and Science University, Portland, Oregon 97239, USA
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24
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Identification and characterization of tyrosine kinases in anole lizard indicate the conserved tyrosine kinase repertoire in vertebrates. Mol Genet Genomics 2017; 292:1405-1418. [PMID: 28819830 DOI: 10.1007/s00438-017-1356-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 08/08/2017] [Indexed: 10/19/2022]
Abstract
The tyrosine kinases (TKs) play principal roles in regulation of multicellular aspects of the organism and are implicated in many cancer types and congenital disorders. The anole lizard has recently been introduced as a model organism for laboratory-based studies of organismal function and field studies of ecology and evolution. However, the TK family of anole lizard has not been systematically identified and characterized yet. In this study, we identified 82 TK-encoding genes in the anole lizard genome and classified them into 28 subfamilies through phylogenetic analysis, with no member from ROS and STYK1 subfamilies identified. Although TK domain sequences and domain organization in each subfamily were conserved, the total number of TKs in different species was much variable. In addition, extensive evolutionary analysis in metazoans indicated that TK repertoire in vertebrates tends to be remarkably stable. Phylogenetic analysis of Eph subfamily indicated that the divergence of EphA and EphB occurred prior to the whole genome duplication (WGD) but after the split of Urochordates and vertebrates. Moreover, the expression pattern analysis of lizard TK genes among 9 different tissues showed that 14 TK genes exhibited tissue-specific expression and 6 TK genes were widely expressed. Comparative analysis of TK expression suggested that the tissue specifically expressed genes showed different expression pattern but the widely expressed genes showed similar pattern between anole lizard and human. These results may provide insights into the evolutionary diversification of animal TK genes and would aid future studies on TK protein regulation of key growth and developmental processes.
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25
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Molecularly targeted drug combinations demonstrate selective effectiveness for myeloid- and lymphoid-derived hematologic malignancies. Proc Natl Acad Sci U S A 2017; 114:E7554-E7563. [PMID: 28784769 DOI: 10.1073/pnas.1703094114] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Translating the genetic and epigenetic heterogeneity underlying human cancers into therapeutic strategies is an ongoing challenge. Large-scale sequencing efforts have uncovered a spectrum of mutations in many hematologic malignancies, including acute myeloid leukemia (AML), suggesting that combinations of agents will be required to treat these diseases effectively. Combinatorial approaches will also be critical for combating the emergence of genetically heterogeneous subclones, rescue signals in the microenvironment, and tumor-intrinsic feedback pathways that all contribute to disease relapse. To identify novel and effective drug combinations, we performed ex vivo sensitivity profiling of 122 primary patient samples from a variety of hematologic malignancies against a panel of 48 drug combinations. The combinations were designed as drug pairs that target nonoverlapping biological pathways and comprise drugs from different classes, preferably with Food and Drug Administration approval. A combination ratio (CR) was derived for each drug pair, and CRs were evaluated with respect to diagnostic categories as well as against genetic, cytogenetic, and cellular phenotypes of specimens from the two largest disease categories: AML and chronic lymphocytic leukemia (CLL). Nearly all tested combinations involving a BCL2 inhibitor showed additional benefit in patients with myeloid malignancies, whereas select combinations involving PI3K, CSF1R, or bromodomain inhibitors showed preferential benefit in lymphoid malignancies. Expanded analyses of patients with AML and CLL revealed specific patterns of ex vivo drug combination efficacy that were associated with select genetic, cytogenetic, and phenotypic disease subsets, warranting further evaluation. These findings highlight the heuristic value of an integrated functional genomic approach to the identification of novel treatment strategies for hematologic malignancies.
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26
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Gordon MJ, Tardi P, Loriaux MM, Spurgeon SE, Traer E, Kovacsovics T, Mayer LD, Tyner JW. CPX-351 exhibits potent and direct ex vivo cytotoxicity against AML blasts with enhanced efficacy for cells harboring the FLT3-ITD mutation. Leuk Res 2016; 53:39-49. [PMID: 28013106 DOI: 10.1016/j.leukres.2016.12.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Revised: 12/08/2016] [Accepted: 12/10/2016] [Indexed: 12/23/2022]
Abstract
PURPOSE Identify AML patients most likely to respond to CPX-351, a nano-scale liposome formulation containing cytarabine and daunorubicin co-encapsulated at a 5:1 molar ratio. METHODS We examined the ex vivo cytotoxic activity of CPX-351 against leukemic cells isolated from 53 AML patients and an additional 127 samples including acute lymphoblastic leukemia, myelodysplastic syndrome/myeloproliferative neoplasms, or chronic lymphocytic leukemia/lymphoma. We assessed activity with respect to common molecular lesions and used flow cytometry to assess CPX-351 cellular uptake. RESULTS AML specimen sensitivity to CPX-351 was similar across conventional risk groups. FLT3-ITD cases were five-fold more sensitive to CPX-351. CPX-351 was active across other indications with nearly all cases exhibiting IC50 values markedly lower than reported 72-h plasma drug concentration in patients receiving CPX-351. The range and distribution of CPX-351 IC50 values were comparable for AML, CLL, and ALL, whereas MDS/MPN cases were less sensitive. CPX-351 uptake analysis revealed a correlation between uptake of CPX-351 and cytotoxic potency. CONCLUSIONS Our findings are consistent with clinical data, in which CPX-351 activity is retained in high-risk AML patients. Ex vivo analysis of cytotoxic potency may provide a means to identify specific AML subsets, such as FLT3-ITD, that benefit most from CPX-351 and warrant additional clinical evaluation.
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Affiliation(s)
- Max J Gordon
- Department of Internal Medicine, Oregon Health & Sciences University, Portland, OR, USA
| | - Paul Tardi
- Jazz Pharmaceuticals, Suite 250 - 887 Great Northern Way, Vancouver, BC V5T 4T5, Canada
| | - Marc M Loriaux
- Department of Pathology, Oregon Health & Science University, Portland, OR, USA; Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Stephen E Spurgeon
- Division of Hematology & Medical Oncology, Oregon Health & Science University, Portland, OR, USA; Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Elie Traer
- Division of Hematology & Medical Oncology, Oregon Health & Science University, Portland, OR, USA; Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Tibor Kovacsovics
- Division of Hematology and Hematologic Malignancies, Huntsman Cancer Institute, Huntsman Cancer Hospital, The University of Utah, Salt Lake City, USA
| | - Lawrence D Mayer
- Jazz Pharmaceuticals, Suite 250 - 887 Great Northern Way, Vancouver, BC V5T 4T5, Canada
| | - 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.
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27
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Histone deacetylase inhibitors induce proteolysis of activated CDC42-associated kinase-1 in leukemic cells. J Cancer Res Clin Oncol 2016; 142:2263-73. [PMID: 27576506 DOI: 10.1007/s00432-016-2229-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 08/22/2016] [Indexed: 12/19/2022]
Abstract
PURPOSE Activated CDC42-associated kinase-1 (ACK1/TNK2) and epigenetic regulators of the histone deacetylase (HDAC) family regulate the proliferation and survival of leukemic cells. 18 HDACs fall into four classes (I-IV). We tested the impact of clinically relevant histone deacetylase inhibitors (HDACi) on ACK1 and if such drugs combine favorably with the therapeutically used ACK1 inhibitor Dasatinib. METHODS We applied the broad-range HDACi Panobinostat/LBH589 and the class I HDAC-specific inhibitor Entinostat/MS-275 to various acute and chronic myeloid leukemia cells (AML/CML). We also used the replicative stress inducer Hydroxyurea (HU), a standard drug for leukemic patients, and the apoptosis inducer Staurosporine (STS). To assess cytotoxic effects of HDACi, we measured cell cycle profiles and DNA fragmentation by flow cytometry. Western blot was employed to analyze protein expression and phosphorylation. RESULTS LBH589 and MS-275 induce proteolysis of ACK1 in CML and AML cells. Panobinostat more strongly induces apoptosis than Entinostat, and this correlates with a significantly pronounced loss of ACK1. STS and HU also propel the degradation of ACK1 in leukemic cells. Moreover, the caspase inhibitor z-VAD-FMK reduces ACK1 degradation in the presence of HDACi. Concomitant with the attenuation of ACK1, we noticed decreased phosphorylation of STAT3. Direct inhibition of ACK1 with Dasatinib also suppresses STAT3 phosphorylation. Furthermore, Dasatinib and HDACi combinations are effective against CML cells. CONCLUSION HDACs sustain the ACK1-STAT3 signaling node and leukemic cell growth. Consistent with their different effects on ACK1 stability or auto-phosphorylation, Dasatinib and HDACi combinations produce beneficial antileukemic effects.
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