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Joglekar T, Chin A, Voskanian-Kordi A, Baek S, Raja A, Rege A, Huang W, Kane M, Laiho M, Webb TR, Fan X, Rubenstein M, Bieberich CJ, Li X. Deep PIM kinase substrate profiling reveals new rational cotherapeutic strategies for acute myeloid leukemia. Blood Adv 2024; 8:3880-3892. [PMID: 38739710 PMCID: PMC11321302 DOI: 10.1182/bloodadvances.2022008144] [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: 05/24/2022] [Revised: 03/05/2024] [Accepted: 04/15/2024] [Indexed: 05/16/2024] Open
Abstract
ABSTRACT Provirus integration site for Moloney murine leukemia virus (PIM) family serine/threonine kinases perform protumorigenic functions in hematologic malignancies and solid tumors by phosphorylating substrates involved in tumor metabolism, cell survival, metastasis, inflammation, and immune cell invasion. However, a comprehensive understanding of PIM kinase functions is currently lacking. Multiple small-molecule PIM kinase inhibitors are currently being evaluated as cotherapeutics in patients with cancer. To further illuminate PIM kinase functions in cancer, we deeply profiled PIM1 substrates using the reverse in-gel kinase assay to identify downstream cellular processes targetable with small molecules. Pathway analyses of putative PIM substrates nominated RNA splicing and ribosomal RNA (rRNA) processing as PIM-regulated cellular processes. PIM inhibition elicited reproducible splicing changes in PIM-inhibitor-responsive acute myeloid leukemia (AML) cell lines. PIM inhibitors synergized with splicing modulators targeting splicing factor 3b subunit 1 (SF3B1) and serine-arginine protein kinase 1 (SRPK1) to kill AML cells. PIM inhibition also altered rRNA processing, and PIM inhibitors synergized with an RNA polymerase I inhibitor to kill AML cells and block AML tumor growth. These data demonstrate that deep kinase substrate knowledge can illuminate unappreciated kinase functions, nominating synergistic cotherapeutic strategies. This approach may expand the cotherapeutic armamentarium to overcome kinase inhibitor-resistant disease that limits durable responses in malignant disease.
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Affiliation(s)
- Tejashree Joglekar
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD
| | - Alexander Chin
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD
| | - Alin Voskanian-Kordi
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD
| | - Seungchul Baek
- Department of Mathematics and Statistics, University of Maryland, Baltimore County, Baltimore, MD
| | - Azim Raja
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD
| | - Apurv Rege
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD
| | - Weiliang Huang
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Baltimore, MD
| | - Maureen Kane
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Baltimore, MD
| | - Marikki Laiho
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, MD
| | | | - Xiaoxuan Fan
- Department of Microbiology and Immunology, University of Maryland Baltimore School of Medicine, Baltimore, MD
- University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD
| | - Michael Rubenstein
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD
| | - Charles J. Bieberich
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD
- Department of Microbiology and Immunology, University of Maryland Baltimore School of Medicine, Baltimore, MD
| | - Xiang Li
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD
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2
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Cui H, Maan H, Vladoiu MC, Zhang J, Taylor MD, Wang B. DeepVelo: deep learning extends RNA velocity to multi-lineage systems with cell-specific kinetics. Genome Biol 2024; 25:27. [PMID: 38243313 PMCID: PMC10799431 DOI: 10.1186/s13059-023-03148-9] [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: 09/26/2023] [Accepted: 12/18/2023] [Indexed: 01/21/2024] Open
Abstract
Existing RNA velocity estimation methods strongly rely on predefined dynamics and cell-agnostic constant transcriptional kinetic rates, assumptions often violated in complex and heterogeneous single-cell RNA sequencing (scRNA-seq) data. Using a graph convolution network, DeepVelo overcomes these limitations by generalizing RNA velocity to cell populations containing time-dependent kinetics and multiple lineages. DeepVelo infers time-varying cellular rates of transcription, splicing, and degradation, recovers each cell's stage in the differentiation process, and detects functionally relevant driver genes regulating these processes. Application to various developmental and pathogenic processes demonstrates DeepVelo's capacity to study complex differentiation and lineage decision events in heterogeneous scRNA-seq data.
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Affiliation(s)
- Haotian Cui
- Peter Munk Cardiac Center, University Health Network, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
- Vector Institute, Toronto, Ontario, Canada
| | - Hassaan Maan
- Peter Munk Cardiac Center, University Health Network, Toronto, Ontario, Canada
- Vector Institute, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Maria C Vladoiu
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Jiao Zhang
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Michael D Taylor
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Baylor College of Medicine, Houston, TX, USA
- Texas Children's Hospital, Houston, TX, USA
| | - Bo Wang
- Peter Munk Cardiac Center, University Health Network, Toronto, Ontario, Canada.
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.
- Vector Institute, Toronto, Ontario, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.
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3
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Stephenson EH, Higgins JMG. Pharmacological approaches to understanding protein kinase signaling networks. Front Pharmacol 2023; 14:1310135. [PMID: 38164473 PMCID: PMC10757940 DOI: 10.3389/fphar.2023.1310135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 11/27/2023] [Indexed: 01/03/2024] Open
Abstract
Protein kinases play vital roles in controlling cell behavior, and an array of kinase inhibitors are used successfully for treatment of disease. Typical drug development pipelines involve biological studies to validate a protein kinase target, followed by the identification of small molecules that effectively inhibit this target in cells, animal models, and patients. However, it is clear that protein kinases operate within complex signaling networks. These networks increase the resilience of signaling pathways, which can render cells relatively insensitive to inhibition of a single kinase, and provide the potential for pathway rewiring, which can result in resistance to therapy. It is therefore vital to understand the properties of kinase signaling networks in health and disease so that we can design effective multi-targeted drugs or combinations of drugs. Here, we outline how pharmacological and chemo-genetic approaches can contribute to such knowledge, despite the known low selectivity of many kinase inhibitors. We discuss how detailed profiling of target engagement by kinase inhibitors can underpin these studies; how chemical probes can be used to uncover kinase-substrate relationships, and how these tools can be used to gain insight into the configuration and function of kinase signaling networks.
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Affiliation(s)
| | - Jonathan M. G. Higgins
- Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle uponTyne, United Kingdom
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4
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Gary CR, Pflum MKH. Kinase-catalyzed Biotinylation with Inactivated Lysates for Discovery of Substrates (K-BILDS). Curr Protoc 2023; 3:e851. [PMID: 37552028 DOI: 10.1002/cpz1.851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/09/2023]
Abstract
Protein phosphorylation is catalyzed by kinases to regulate a large variety of cellular activities, including growth and signal transduction. Methods to identify kinase substrates are crucial to fully understand phosphorylation-mediated cellular events and disease states. Here, we report a set of protocols to identify substrates of a target kinase using Kinase-catalyzed Biotinylation with Inactivated Lysates for Discovery of Substrates (K-BILDS). As described in these protocols, K-BILDS involves inactivation of endogenous kinases in lysates, followed by addition of an active exogenous kinase and the γ-phosphate-modified ATP analog ATP-biotin for kinase-catalyzed biotinylation of cellular substrates. Avidin enrichment isolates biotinylated substrates of the active kinase, which can be monitored by western blot. Substrates of the target kinase can also be discovered using mass spectrometry analysis. Key advantages of K-BILDS include compatibility with any lysate, tissue homogenate, or complex mixture of biological relevance and any active kinase of interest. K-BILDS is a versatile method for studying or discovering substrates of a kinase of interest to characterize biological pathways thoroughly. © 2023 Wiley Periodicals LLC. Basic Protocol 1: FSBA treatment of lysates to inactivate kinases Basic Protocol 2: Kinase-catalyzed Biotinylation with Inactivated Lysates for Discovery of Substrates (K-BILDS).
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Affiliation(s)
- Chelsea R Gary
- Department of Chemistry, Wayne State University, Detroit, Michigan
| | - Mary Kay H Pflum
- Department of Chemistry, Wayne State University, Detroit, Michigan
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5
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DeMarco AG, Hall MC. Phosphoproteomic Approaches for Identifying Phosphatase and Kinase Substrates. Molecules 2023; 28:3675. [PMID: 37175085 PMCID: PMC10180314 DOI: 10.3390/molecules28093675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 04/21/2023] [Accepted: 04/22/2023] [Indexed: 05/15/2023] Open
Abstract
Protein phosphorylation is a ubiquitous post-translational modification controlled by the opposing activities of protein kinases and phosphatases, which regulate diverse biological processes in all kingdoms of life. One of the key challenges to a complete understanding of phosphoregulatory networks is the unambiguous identification of kinase and phosphatase substrates. Liquid chromatography-coupled mass spectrometry (LC-MS/MS) and associated phosphoproteomic tools enable global surveys of phosphoproteome changes in response to signaling events or perturbation of phosphoregulatory network components. Despite the power of LC-MS/MS, it is still challenging to directly link kinases and phosphatases to specific substrate phosphorylation sites in many experiments. Here, we survey common LC-MS/MS-based phosphoproteomic workflows for identifying protein kinase and phosphatase substrates, noting key advantages and limitations of each. We conclude by discussing the value of inducible degradation technologies coupled with phosphoproteomics as a new approach that overcomes some limitations of current methods for substrate identification of kinases, phosphatases, and other regulatory enzymes.
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Affiliation(s)
- Andrew G. DeMarco
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Mark C. Hall
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
- Institute for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
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6
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Martin MP, Noble MEM. Exiting the tunnel of uncertainty: crystal soak to validated hit. Acta Crystallogr D Struct Biol 2022; 78:1294-1302. [PMID: 36322414 PMCID: PMC9629488 DOI: 10.1107/s2059798322009986] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 10/12/2022] [Indexed: 11/28/2022] Open
Abstract
Crystallographic fragment screens provide an efficient and effective way to identify small-molecule ligands of a crystallized protein. Due to their low molecular weight, such hits tend to have low, often unquantifiable, affinity for their target, complicating the twin challenges of validating the hits as authentic solution-phase ligands of the target and identifying the `best' hit(s) for further elaboration. In this article, approaches that address these challenges are assessed. Using retrospective analysis of a recent ATAD2 hit-identification campaign, alongside other examples of successful fragment-screening campaigns, it is suggested that hit validation and prioritization are best achieved by a `triangulation' approach in which the results of multiple available biochemical and biophysical techniques are correlated to develop qualitative structure-activity relationships (SARs). Such qualitative SARs may indeed be the only means by which to navigate a project through the tunnel of uncertainty that prevails before on-scale biophysical, biochemical and/or biological measurements become possible.
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Affiliation(s)
- Mathew P. Martin
- Cancer Research UK Drug Discovery Unit, Newcastle University, Paul O’Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Martin E. M. Noble
- Cancer Research UK Drug Discovery Unit, Newcastle University, Paul O’Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4HH, United Kingdom
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7
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SILAC kinase screen identifies potential MASTL substrates. Sci Rep 2022; 12:10568. [PMID: 35732702 PMCID: PMC9217955 DOI: 10.1038/s41598-022-14933-0] [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: 03/30/2022] [Accepted: 06/15/2022] [Indexed: 12/04/2022] Open
Abstract
Microtubule-associated serine/threonine kinase-like (MASTL) has emerged as a critical regulator of mitosis and as a potential oncogene in a variety of cancer types. To date, Arpp-19/ENSA are the only known substrates of MASTL. However, with the roles of MASTL expanding and increased interest in development of MASTL inhibitors, it has become critical to determine if there are additional substrates and what the optimal consensus motif for MASTL is. Here we utilized a whole cell lysate in vitro kinase screen combined with stable isotope labelling of amino acids in cell culture (SILAC) to identify potential substrates and the residue preference of MASTL. Using the related AGC kinase family members AKT1/2, the kinase screen identified several known and new substrates highly enriched for the validated consensus motif of AKT. Applying this method to MASTL identified 59 phospho-sites on 67 proteins that increased in the presence of active MASTL. Subsequent in vitro kinase assays suggested that MASTL may phosphorylate hnRNPM, YB1 and TUBA1C under certain in vitro conditions. Taken together, these data suggest that MASTL may phosphorylate several additional substrates, providing insight into the ever-increasing biological functions and roles MASTL plays in driving cancer progression and therapy resistance.
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8
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Salokas K, Liu X, Öhman T, Chowdhury I, Gawriyski L, Keskitalo S, Varjosalo M. Physical and functional interactome atlas of human receptor tyrosine kinases. EMBO Rep 2022; 23:e54041. [PMID: 35384245 PMCID: PMC9171411 DOI: 10.15252/embr.202154041] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 03/03/2022] [Accepted: 03/09/2022] [Indexed: 12/03/2022] Open
Abstract
Much cell-to-cell communication is facilitated by cell surface receptor tyrosine kinases (RTKs). These proteins phosphorylate their downstream cytoplasmic substrates in response to stimuli such as growth factors. Despite their central roles, the functions of many RTKs are still poorly understood. To resolve the lack of systematic knowledge, we apply three complementary methods to map the molecular context and substrate profiles of RTKs. We use affinity purification coupled to mass spectrometry (AP-MS) to characterize stable binding partners and RTK-protein complexes, proximity-dependent biotin identification (BioID) to identify transient and proximal interactions, and an in vitro kinase assay to identify RTK substrates. To identify how kinase interactions depend on kinase activity, we also use kinase-deficient mutants. Our data represent a comprehensive, systemic mapping of RTK interactions and substrates. This resource adds information regarding well-studied RTKs, offers insights into the functions of less well-studied RTKs, and highlights RTK-RTK interactions and shared signaling pathways.
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Affiliation(s)
- Kari Salokas
- Institute of BiotechnologyHiLIFEUniversity of HelsinkiHelsinkiFinland
| | - Xiaonan Liu
- Institute of BiotechnologyHiLIFEUniversity of HelsinkiHelsinkiFinland
| | - Tiina Öhman
- Institute of BiotechnologyHiLIFEUniversity of HelsinkiHelsinkiFinland
| | | | - Lisa Gawriyski
- Institute of BiotechnologyHiLIFEUniversity of HelsinkiHelsinkiFinland
| | - Salla Keskitalo
- Institute of BiotechnologyHiLIFEUniversity of HelsinkiHelsinkiFinland
| | - Markku Varjosalo
- Institute of BiotechnologyHiLIFEUniversity of HelsinkiHelsinkiFinland
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9
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Haas TM, Mundinger S, Qiu D, Jork N, Ritter K, Dürr‐Mayer T, Ripp A, Saiardi A, Schaaf G, Jessen HJ. Stable Isotope Phosphate Labelling of Diverse Metabolites is Enabled by a Family of 18O-Phosphoramidites. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 134:e202112457. [PMID: 38505299 PMCID: PMC10947094 DOI: 10.1002/ange.202112457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Indexed: 11/09/2022]
Abstract
Stable isotope labelling is state-of-the-art in quantitative mass spectrometry, yet often accessing the required standards is cumbersome and very expensive. Here, a unifying synthetic concept for 18O-labelled phosphates is presented, based on a family of modified 18O2-phosphoramidite reagents. This toolbox offers access to major classes of biologically highly relevant phosphorylated metabolites as their isotopologues including nucleotides, inositol phosphates, -pyrophosphates, and inorganic polyphosphates. 18O-enrichment ratios >95 % and good yields are obtained consistently in gram-scale reactions, while enabling late-stage labelling. We demonstrate the utility of the 18O-labelled inositol phosphates and pyrophosphates by assignment of these metabolites from different biological matrices. We demonstrate that phosphate neutral loss is negligible in an analytical setup employing capillary electrophoresis electrospray ionisation triple quadrupole mass spectrometry.
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Affiliation(s)
- Thomas M. Haas
- Institute of Organic ChemistryAlbert-Ludwigs-Universität FreiburgAlbertstrasse 2179102Freiburg im BreisgauGermany
| | - Stephan Mundinger
- Institute of Organic ChemistryAlbert-Ludwigs-Universität FreiburgAlbertstrasse 2179102Freiburg im BreisgauGermany
| | - Danye Qiu
- Institute of Organic ChemistryAlbert-Ludwigs-Universität FreiburgAlbertstrasse 2179102Freiburg im BreisgauGermany
| | - Nikolaus Jork
- Institute of Organic ChemistryAlbert-Ludwigs-Universität FreiburgAlbertstrasse 2179102Freiburg im BreisgauGermany
- CIBSS—The Center for Biological Signaling Studies &, Spemann Graduate School of Biology and Medicine (SGBM)Albert-Ludwigs-Universität FreiburgGermany
| | - Kevin Ritter
- Institute of Organic ChemistryAlbert-Ludwigs-Universität FreiburgAlbertstrasse 2179102Freiburg im BreisgauGermany
| | - Tobias Dürr‐Mayer
- Institute of Organic ChemistryAlbert-Ludwigs-Universität FreiburgAlbertstrasse 2179102Freiburg im BreisgauGermany
| | - Alexander Ripp
- Institute of Organic ChemistryAlbert-Ludwigs-Universität FreiburgAlbertstrasse 2179102Freiburg im BreisgauGermany
| | - Adolfo Saiardi
- Medical Research Council, Laboratory for molecular Cell BiologyUniversity College LondonUK
| | - Gabriel Schaaf
- INRES—Institut für Nutzpflanzenwissenschaften und RessourcenschutzUniversität BonnKarlrobert-Kreiten-Strasse 1353115BonnGermany
| | - Henning J. Jessen
- Institute of Organic ChemistryAlbert-Ludwigs-Universität FreiburgAlbertstrasse 2179102Freiburg im BreisgauGermany
- CIBSS—The Center for Biological Signaling Studies &, Spemann Graduate School of Biology and Medicine (SGBM)Albert-Ludwigs-Universität FreiburgGermany
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10
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Haas TM, Mundinger S, Qiu D, Jork N, Ritter K, Dürr‐Mayer T, Ripp A, Saiardi A, Schaaf G, Jessen HJ. Stable Isotope Phosphate Labelling of Diverse Metabolites is Enabled by a Family of 18 O-Phosphoramidites. Angew Chem Int Ed Engl 2022; 61:e202112457. [PMID: 34734451 PMCID: PMC9298905 DOI: 10.1002/anie.202112457] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Indexed: 11/12/2022]
Abstract
Stable isotope labelling is state-of-the-art in quantitative mass spectrometry, yet often accessing the required standards is cumbersome and very expensive. Here, a unifying synthetic concept for 18 O-labelled phosphates is presented, based on a family of modified 18 O2 -phosphoramidite reagents. This toolbox offers access to major classes of biologically highly relevant phosphorylated metabolites as their isotopologues including nucleotides, inositol phosphates, -pyrophosphates, and inorganic polyphosphates. 18 O-enrichment ratios >95 % and good yields are obtained consistently in gram-scale reactions, while enabling late-stage labelling. We demonstrate the utility of the 18 O-labelled inositol phosphates and pyrophosphates by assignment of these metabolites from different biological matrices. We demonstrate that phosphate neutral loss is negligible in an analytical setup employing capillary electrophoresis electrospray ionisation triple quadrupole mass spectrometry.
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Affiliation(s)
- Thomas M. Haas
- Institute of Organic ChemistryAlbert-Ludwigs-Universität FreiburgAlbertstrasse 2179102Freiburg im BreisgauGermany
| | - Stephan Mundinger
- Institute of Organic ChemistryAlbert-Ludwigs-Universität FreiburgAlbertstrasse 2179102Freiburg im BreisgauGermany
| | - Danye Qiu
- Institute of Organic ChemistryAlbert-Ludwigs-Universität FreiburgAlbertstrasse 2179102Freiburg im BreisgauGermany
| | - Nikolaus Jork
- Institute of Organic ChemistryAlbert-Ludwigs-Universität FreiburgAlbertstrasse 2179102Freiburg im BreisgauGermany
- CIBSS—The Center for Biological Signaling Studies &, Spemann Graduate School of Biology and Medicine (SGBM)Albert-Ludwigs-Universität FreiburgGermany
| | - Kevin Ritter
- Institute of Organic ChemistryAlbert-Ludwigs-Universität FreiburgAlbertstrasse 2179102Freiburg im BreisgauGermany
| | - Tobias Dürr‐Mayer
- Institute of Organic ChemistryAlbert-Ludwigs-Universität FreiburgAlbertstrasse 2179102Freiburg im BreisgauGermany
| | - Alexander Ripp
- Institute of Organic ChemistryAlbert-Ludwigs-Universität FreiburgAlbertstrasse 2179102Freiburg im BreisgauGermany
| | - Adolfo Saiardi
- Medical Research Council, Laboratory for molecular Cell BiologyUniversity College LondonUK
| | - Gabriel Schaaf
- INRES—Institut für Nutzpflanzenwissenschaften und RessourcenschutzUniversität BonnKarlrobert-Kreiten-Strasse 1353115BonnGermany
| | - Henning J. Jessen
- Institute of Organic ChemistryAlbert-Ludwigs-Universität FreiburgAlbertstrasse 2179102Freiburg im BreisgauGermany
- CIBSS—The Center for Biological Signaling Studies &, Spemann Graduate School of Biology and Medicine (SGBM)Albert-Ludwigs-Universität FreiburgGermany
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11
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Rajendran S, Swaroop SS, Roy J, Inemai E, Murugan S, Rayala SK, Venkatraman G. p21 activated kinase-1 and tamoxifen - A deadly nexus impacting breast cancer outcomes. Biochim Biophys Acta Rev Cancer 2021; 1877:188668. [PMID: 34896436 DOI: 10.1016/j.bbcan.2021.188668] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 12/03/2021] [Accepted: 12/03/2021] [Indexed: 12/18/2022]
Abstract
Tamoxifen is a commonly used drug in the treatment of ER + ve breast cancers since 1970. However, development of resistance towards tamoxifen limits its remarkable clinical success. In this review, we have attempted to provide a brief overview of multiple mechanism that may lead to tamoxifen resistance, with a special emphasis on the roles played by the oncogenic kinase- PAK1. Analysing the genomic data sets available in the cBioPortal, we found that PAK1 gene amplification significantly affects the Relapse Free Survival of the ER + ve breast cancer patients. While PAK1 is known to promote tamoxifen resistance by phosphorylating ERα at Ser305, existing literature suggests that PAK1 can fuel up tamoxifen resistance obliquely by phosphorylating other substrates. We have summarised some of the approaches in the mass spectrometry based proteomics, which would enable us to study the tamoxifen resistance specific phosphoproteomic landscape of PAK1. We also propose that elucidating the multiple mechanisms by which PAK1 promotes tamoxifen resistance might help us discover druggable targets and biomarkers.
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Affiliation(s)
- Swetha Rajendran
- Department of Human Genetics, Sri Ramachandra Faculty of Biomedical Sciences and Technology, Sri Ramachandra Institute of Higher Education and Research, Chennai, India
| | - Srikanth Swamy Swaroop
- Department of Human Genetics, Sri Ramachandra Faculty of Biomedical Sciences and Technology, Sri Ramachandra Institute of Higher Education and Research, Chennai, India
| | - Joydeep Roy
- Department of Biotechnology, Indian Institute of Technology, Madras, Chennai, India
| | - Ezhil Inemai
- Department of Biotechnology, Indian Institute of Technology, Madras, Chennai, India
| | - Sowmiya Murugan
- Department of Biotechnology, Indian Institute of Technology, Madras, Chennai, India
| | - Suresh K Rayala
- Department of Biotechnology, Indian Institute of Technology, Madras, Chennai, India.
| | - Ganesh Venkatraman
- Department of Human Genetics, Sri Ramachandra Faculty of Biomedical Sciences and Technology, Sri Ramachandra Institute of Higher Education and Research, Chennai, India.
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12
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Phosphoproteomics Meets Chemical Genetics: Approaches for Global Mapping and Deciphering the Phosphoproteome. Int J Mol Sci 2020; 21:ijms21207637. [PMID: 33076458 PMCID: PMC7588962 DOI: 10.3390/ijms21207637] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/13/2020] [Accepted: 10/14/2020] [Indexed: 12/14/2022] Open
Abstract
Protein kinases are important enzymes involved in the regulation of various cellular processes. To function properly, each protein kinase phosphorylates only a limited number of proteins among the thousands present in the cell. This provides a rapid and dynamic regulatory mechanism that controls biological functions of the proteins. Despite the importance of protein kinases, most of their substrates remain unknown. Recently, the advances in the fields of protein engineering, chemical genetics, and mass spectrometry have boosted studies on identification of bona fide substrates of protein kinases. Among the various methods in protein kinase specific substrate identification, genetically engineered protein kinases and quantitative phosphoproteomics have become promising tools. Herein, we review the current advances in the field of chemical genetics in analog-sensitive protein kinase mutants and highlight selected strategies for identifying protein kinase substrates and studying the dynamic nature of protein phosphorylation.
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13
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Haas TM, Qiu D, Häner M, Angebauer L, Ripp A, Singh J, Koch HG, Jessen-Trefzer C, Jessen HJ. Four Phosphates at One Blow: Access to Pentaphosphorylated Magic Spot Nucleotides and Their Analysis by Capillary Electrophoresis. J Org Chem 2020; 85:14496-14506. [PMID: 32502348 PMCID: PMC7684580 DOI: 10.1021/acs.joc.0c00841] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
The
complex phosphorylation pattern of natural and modified pentaphosphorylated
magic spot nucleotides is generated in a highly efficient way. A cyclic
pyrophosphoryl phosphoramidite (cPyPA) reagent is used to introduce
four phosphates on nucleosides regioselectively in a one-flask key
transformation. The obtained magic spot nucleotides are used to develop
a capillary electrophoresis UV detection method, enabling nucleotide
assignment in complex bacterial extracts.
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Affiliation(s)
- Thomas M Haas
- Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
| | - Danye Qiu
- Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
| | - Markus Häner
- Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
| | - Larissa Angebauer
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany.,Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Alexander Ripp
- Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
| | - Jyoti Singh
- Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
| | - Hans-Georg Koch
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Claudia Jessen-Trefzer
- Institute of Pharmaceutical Biology and Biotechnology, University of Freiburg, 79104 Freiburg, Germany
| | - Henning J Jessen
- Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany.,CIBSS, Centre for Integrative Biological Signaling Studies, University of Freiburg, 79104 Freiburg, Germany
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14
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Advances in defining signaling networks for the establishment of neuronal polarity. Curr Opin Cell Biol 2020; 63:76-87. [DOI: 10.1016/j.ceb.2019.12.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 12/22/2019] [Accepted: 12/24/2019] [Indexed: 12/18/2022]
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15
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Arrington J, Xue L, Wang WH, Geahlen RL, Tao WA. Identification of the Direct Substrates of the ABL Kinase via Kinase Assay Linked Phosphoproteomics with Multiple Drug Treatments. J Proteome Res 2019; 18:1679-1690. [PMID: 30869898 DOI: 10.1021/acs.jproteome.8b00942] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Ableson tyrosine kinase (ABL) plays essential roles in cell differentiation, division, adhesion, and stress response. However, fusion of the breakpoint cluster region (BCR) to ABL produces constitutive kinase activity that causes chronic myelogenous leukemia (CML). Small molecule tyrosine kinase inhibitors (TKIs) such as imatinib revolutionized the treatment of CML and other cancers, but acquired resistance to these inhibitors is rising. Thus, careful dissection of ABL signaling pathways is needed to find novel drug targets. Here we present a refined proteomic approach for elucidation of direct kinase substrates called kinase assay linked phosphoproteomics (KALIP). Our strategy integrates in vitro kinase assays at both the peptide and protein levels with quantitative tyrosine phosphoproteomics in response to treatment by multiple TKIs. Utilizing multiple TKIs permits elimination of off-target effects of these drugs, and overlapping the in vivo and in vitro data sets allows us to define a list of the most probable kinase substrates. Applying our approach produced a list of 60 ABL substrates, including novel and known proteins. We demonstrate that spleen tyrosine kinase (SYK) is a novel direct substrate of ABL, and we predict our proteomic strategy may facilitate identification of substrates in other cancers that have disrupted kinase signaling.
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16
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Shah K, Kim H. The significant others: Global search for direct kinase substrates using chemical approaches. IUBMB Life 2019; 71:721-737. [PMID: 30801966 DOI: 10.1002/iub.2023] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 01/27/2019] [Indexed: 12/16/2022]
Abstract
Protein kinases function as key signaling hubs in the intricate network of biochemical signaling processes in the living cell. More than two-thirds of the human proteome is estimated to be phosphorylated at ~960,000 phosphosites, which makes it challenging to identify the direct contribution of any desired kinase in generating this phosphoproteome. In this review, we discuss some of the methods that have been developed over the years for global identification of kinase substrates. The methods are essentially categorized into two classes, namely, (i) direct tagging of kinase substrates and (ii) indirect phosphoproteomics-based approaches. We discuss the advantages and limitations entailed to each of the method introduced, with a special emphasis on the analog-sensitive (as) kinase approach method. © 2019 IUBMB Life, 71(6):721-737, 2019.
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Affiliation(s)
- Kavita Shah
- Department of Chemistry and Purdue University Center for Cancer Research, Purdue University, 560 Oval Drive, West Lafayette, IN 47907, USA
| | - Hyunjin Kim
- Department of Chemistry and Purdue University Center for Cancer Research, Purdue University, 560 Oval Drive, West Lafayette, IN 47907, USA
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17
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Ayati M, Wiredja D, Schlatzer D, Maxwell S, Li M, Koyutürk M, Chance MR. CoPhosK: A method for comprehensive kinase substrate annotation using co-phosphorylation analysis. PLoS Comput Biol 2019; 15:e1006678. [PMID: 30811403 PMCID: PMC6411229 DOI: 10.1371/journal.pcbi.1006678] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 03/11/2019] [Accepted: 11/26/2018] [Indexed: 12/30/2022] Open
Abstract
We present CoPhosK to predict kinase-substrate associations for phosphopeptide substrates detected by mass spectrometry (MS). The tool utilizes a Naïve Bayes framework with priors of known kinase-substrate associations (KSAs) to generate its predictions. Through the mining of MS data for the collective dynamic signatures of the kinases' substrates revealed by correlation analysis of phosphopeptide intensity data, the tool infers KSAs in the data for the considerable body of substrates lacking such annotations. We benchmarked the tool against existing approaches for predicting KSAs that rely on static information (e.g. sequences, structures and interactions) using publically available MS data, including breast, colon, and ovarian cancer models. The benchmarking reveals that co-phosphorylation analysis can significantly improve prediction performance when static information is available (about 35% of sites) while providing reliable predictions for the remainder, thus tripling the KSAs available from the experimental MS data providing to a comprehensive and reliable characterization of the landscape of kinase-substrate interactions well beyond current limitations.
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Affiliation(s)
- Marzieh Ayati
- Department of Electrical Engineering and Computer Science, Case Western Reserve University, Cleveland, OH
- Department of Computer Science, University of Texas Rio Grande Valley, Edinburg, TX
| | - Danica Wiredja
- Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, OH
| | - Daniela Schlatzer
- Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, OH
| | - Sean Maxwell
- Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, OH
| | - Ming Li
- Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, OH
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH
| | - Mehmet Koyutürk
- Department of Electrical Engineering and Computer Science, Case Western Reserve University, Cleveland, OH
- Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, OH
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH
| | - Mark R. Chance
- Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, OH
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH
- Department of Nutrition, Case Western Reserve University, Cleveland, OH
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18
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Abstract
Protein phosphorylation is a dynamic post-translational modification critical for biological responses. At the level of individual molecules, phosphorylation dynamics can have important functional implications, but this information is rarely quantified. We discuss how rapid phosphorylation-dephosphorylation cycles could underlie important signaling properties, including the ability to rapidly bind and release proteins.
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Affiliation(s)
- Lendert Gelens
- Laboratory of Dynamics in Biological Systems, Department of Cellular and Molecular Medicine, University of Leuven, 3000 Leuven, Belgium
| | - Adrian T Saurin
- School of Medicine, Jacqui Wood Cancer Centre, University of Dundee, Dundee DD1 9SY, UK.
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19
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Meyer NO, O'Donoghue AJ, Schulze-Gahmen U, Ravalin M, Moss SM, Winter MB, Knudsen GM, Craik CS. Multiplex Substrate Profiling by Mass Spectrometry for Kinases as a Method for Revealing Quantitative Substrate Motifs. Anal Chem 2017; 89:4550-4558. [PMID: 28322550 DOI: 10.1021/acs.analchem.6b05002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The more than 500 protein kinases comprising the human kinome catalyze hundreds of thousands of phosphorylation events to regulate a diversity of cellular functions; however, the extended substrate specificity is still unknown for many of these kinases. We report here a method for quantitatively describing kinase substrate specificity using an unbiased peptide library-based approach with direct measurement of phosphorylation by tandem liquid chromatography-tandem mass spectrometry (LC-MS/MS) peptide sequencing (multiplex substrate profiling by mass spectrometry, MSP-MS). This method can be deployed with as low as 10 nM enzyme to determine activity against S/T/Y-containing peptides; additionally, label-free quantitation is used to ascertain catalytic efficiency values for individual peptide substrates in the multiplex assay. Using this approach we developed quantitative motifs for a selection of kinases from each branch of the kinome, with and without known substrates, highlighting the applicability of the method. The sensitivity of this approach is evidenced by its ability to detect phosphorylation events from nanogram quantities of immunoprecipitated material, which allows for wider applicability of this method. To increase the information content of the quantitative kinase motifs, a sublibrary approach was used to expand the testable sequence space within a peptide library of approximately 100 members for CDK1, CDK7, and CDK9. Kinetic analysis of the HIV-1 Tat (transactivator of transcription)-positive transcription elongation factor b (P-TEFb) interaction allowed for localization of the P-TEFb phosphorylation site as well as characterization of the stimulatory effect of Tat on P-TEFb catalytic efficiency.
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Affiliation(s)
- Nicole O Meyer
- Department of Pharmaceutical Chemistry, University of California San Francisco , San Francisco, California 94158, United States
| | - Anthony J O'Donoghue
- Department of Pharmaceutical Chemistry, University of California San Francisco , San Francisco, California 94158, United States
| | - Ursula Schulze-Gahmen
- Department of Molecular and Cell Biology, University of California Berkeley , Berkeley, California 94720, United States
| | - Matthew Ravalin
- Department of Pharmaceutical Chemistry, University of California San Francisco , San Francisco, California 94158, United States
| | - Steven M Moss
- Department of Pharmaceutical Chemistry, University of California San Francisco , San Francisco, California 94158, United States
| | - Michael B Winter
- Department of Pharmaceutical Chemistry, University of California San Francisco , San Francisco, California 94158, United States
| | - Giselle M Knudsen
- Department of Pharmaceutical Chemistry, University of California San Francisco , San Francisco, California 94158, United States
| | - Charles S Craik
- Department of Pharmaceutical Chemistry, University of California San Francisco , San Francisco, California 94158, United States
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20
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Identification of mycobacterial GarA as a substrate of protein kinase G from M. tuberculosis using a KESTREL-based proteome wide approach. J Microbiol Methods 2017; 136:34-39. [PMID: 28249794 DOI: 10.1016/j.mimet.2017.02.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 02/19/2017] [Accepted: 02/24/2017] [Indexed: 11/22/2022]
Abstract
Signal transduction in bacteria is generally mediated via two-component systems. These systems depend on the transfer of a phosphate molecule from a donor to an acceptor by histidine kinases, thereby activating the acceptor to allow downstream signaling/activation. Several bacterial genomes, including the genome of M. tuberculosis, were shown to encode eukaryotic-like kinases. To better understand the function of these kinases and the regulatory networks within which they operate, identification of downstream targets is essential. We here present a straightforward approach for the identification of bacterial Ser/Thr-kinase substrates. This approach is based on the KESTREL (Kinase Tracking and Substrate Elucidation) procedure combined with reversed-phase chromatography and two-dimensional gel electrophoresis. Using this method, GarA was identified as one potential substrate for the mycobacterial Ser/Thr-protein kinase G (PknG). These results show that the modified KESTREL approach can be successfully employed for the identification of substrates for bacterial Ser/Thr-kinases.
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