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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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Comparing the efficacy and selectivity of Ck2 inhibitors. A phosphoproteomics approach. Eur J Med Chem 2021; 214:113217. [PMID: 33548633 DOI: 10.1016/j.ejmech.2021.113217] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/18/2021] [Accepted: 01/18/2021] [Indexed: 01/10/2023]
Abstract
CK2 (an acronym derived from the misnomer "casein kinase 2") denotes a ubiquitous, highly pleiotropic protein kinase which has been implicated in global human pathologies, with special reference to cancer. A large spectrum of fairly selective, cell permeable CK2 inhibitors are available, one of which, CX4945 is already in clinical trials for the treatment of neoplasia. Another recently developed CK2 inhibitor, GO289, displays in vitro potency and selectivity comparable to CX4945. Here the cellular efficiency of these two inhibitors has been evaluated by treating C2C12 myoblasts for 5 h with each of them at 4 μM concentration and running a quantitative phosphoproteomics analysis of phosphosites affected by the two compounds. A small but significant proportion of the quantified phosphosites is decreased by treatment with CX4945 and, even more with GO289. This figure substantially increases if a subset of quantified phosphosites conforming to the CK2 consensus (pS/pT-x-x-D/E/pS/pT) is considered. Also in this case GO289 is more effective than CX4945. By adopting stringent criteria two shortlists of 70 and 35 sites whose phosphorylation is decreased >50% by GO289 and CX4945, respectively, have been generated. All these phosphosites conform to the consensus of CK2 with just sporadic exceptions. Their WebLogos are indistinguishable from that of bona fide CK2 phosphosites and their Two-Sample Logos rule out any significant contribution of Pro-directed and basophilic protein kinases to their generation. To sum up, we can conclude that by treating C2C12 cells for 5 h with either CX4945 or GO289 off-target effects are negligible since almost all the phosphosites undergoing a substantial reduction are attributable to CK2, with a higher inhibitory efficacy displayed by GO289. CX4945 and GO289 provide highly selective tools to control the CK2-dependent phosphoproteome compared with previously developed CK2 inhibitors.
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Li X, Cox JT, Huang W, Kane M, Tang K, Bieberich CJ. Quantifying Kinase-Specific Phosphorylation Stoichiometry Using Stable Isotope Labeling In a Reverse In-Gel Kinase Assay. Anal Chem 2016; 88:11468-11475. [PMID: 27808495 DOI: 10.1021/acs.analchem.6b02599] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Despite recent advancements in large-scale phosphoproteomics, methods to quantify kinase-specific phosphorylation stoichiometry of protein substrates are lacking. We developed a method to quantify kinase-specific phosphorylation stoichiometry by combining the reverse in-gel kinase assay (RIKA) with high-resolution liquid chromatography-mass spectrometry (LC-MS). Beginning with predetermined ratios of phosphorylated to nonphosphorylated protein kinase CK2 (CK2) substrate molecules, we employed 18O-labeled adenosine triphosphate (18O-ATP) as the phosphate donor in a RIKA, then quantified the ratio of 18O- versus 16O-labeled tryptic phosphopeptide using high mass accuracy mass spectrometry (MS). We demonstrate that the phosphorylation stoichiometry determined by this method across a broad percent phosphorylation range correlated extremely well with the predicted value (correlation coefficient = 0.99). This approach provides a quantitative alternative to antibody-based methods of determining the extent of phosphorylation of a substrate pool.
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Affiliation(s)
- Xiang Li
- Department of Biological Sciences, University of Maryland Baltimore County , Baltimore, Maryland 21250, United States
| | - Jonathan T Cox
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
| | - Weiliang Huang
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland , Baltimore, Maryland 21201, United States
| | - Maureen Kane
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland , Baltimore, Maryland 21201, United States
| | - Keqi Tang
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
| | - Charles J Bieberich
- Department of Biological Sciences, University of Maryland Baltimore County , Baltimore, Maryland 21250, United States.,Marlene and Stewart Greenebaum Cancer Center, University of Maryland Baltimore , Baltimore, Maryland 21201, United States
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Perera Y, Pedroso S, Borras-Hidalgo O, Vázquez DM, Miranda J, Villareal A, Falcón V, Cruz LD, Farinas HG, Perea SE. Pharmacologic inhibition of the CK2-mediated phosphorylation of B23/NPM in cancer cells selectively modulates genes related to protein synthesis, energetic metabolism, and ribosomal biogenesis. Mol Cell Biochem 2015; 404:103-12. [DOI: 10.1007/s11010-015-2370-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 02/23/2015] [Indexed: 11/29/2022]
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Blagg J, Workman P. Chemical biology approaches to target validation in cancer. Curr Opin Pharmacol 2014; 17:87-100. [PMID: 25175311 DOI: 10.1016/j.coph.2014.07.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 07/15/2014] [Accepted: 07/16/2014] [Indexed: 02/06/2023]
Abstract
Target validation is a crucial element of drug discovery. Especially given the wealth of potential targets emerging from cancer genome sequencing and functional genetic screens, and also considering the time and cost of downstream drug discovery efforts, it is essential to build confidence in a proposed target, ideally using different technical approaches. We argue that complementary biological and chemical biology strategies are essential for robust target validation. We discuss recent progress in the discovery and application of high quality chemical tools and other chemical biology approaches to target validation in cancer. Among other topical examples, we highlight the emergence of designed irreversible chemical tools to study potential target proteins and oncogenic pathways that were hitherto regarded as poorly druggable.
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Affiliation(s)
- Julian Blagg
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK.
| | - Paul Workman
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK.
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Padmanabhan A, Li X, Bieberich CJ. Protein kinase A regulates MYC protein through transcriptional and post-translational mechanisms in a catalytic subunit isoform-specific manner. J Biol Chem 2013; 288:14158-14169. [PMID: 23504319 PMCID: PMC3656272 DOI: 10.1074/jbc.m112.432377] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 03/11/2013] [Indexed: 11/06/2022] Open
Abstract
MYC levels are tightly regulated in cells, and deregulation is associated with many cancers. In this report, we describe the existence of a MYC-protein kinase A (PKA)-polo-like kinase 1 (PLK1) signaling loop in cells. We report that sequential MYC phosphorylation by PKA and PLK1 protects MYC from proteasome-mediated degradation. Interestingly, short term pan-PKA inhibition diminishes MYC level, whereas prolonged PKA catalytic subunit α (PKACα) knockdown, but not PKA catalytic subunit β (PKACβ) knockdown, increases MYC. We show that the short term effect of pan-PKA inhibition on MYC is post-translational and the PKACα-specific long term effect on MYC is transcriptional. These data also reveal distinct functional roles among PKA catalytic isoforms in MYC regulation. We attribute this effect to differential phosphorylation selectivity among PKA catalytic subunits, which we demonstrate for multiple substrates. Further, we also show that MYC up-regulates PKACβ, transcriptionally forming a proximate positive feedback loop. These results establish PKA as a regulator of MYC and highlight the distinct biological roles of the different PKA catalytic subunits.
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Affiliation(s)
- Achuth Padmanabhan
- Department of Biological Sciences, the University of Maryland Baltimore County, Baltimore, Maryland 21250
| | - Xiang Li
- Department of Biological Sciences, the University of Maryland Baltimore County, Baltimore, Maryland 21250
| | - Charles J Bieberich
- Department of Biological Sciences, the University of Maryland Baltimore County, Baltimore, Maryland 21250; Marlene and Stewart Greenebaum Cancer Center, University of Maryland, Baltimore, Maryland 21201.
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