1
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Kennedy PH, Alborzian Deh Sheikh A, Balakar M, Jones AC, Olive ME, Hegde M, Matias MI, Pirete N, Burt R, Levy J, Little T, Hogan PG, Liu DR, Doench JG, Newton AC, Gottschalk RA, de Boer CG, Alarcón S, Newby GA, Myers SA. Post-translational modification-centric base editor screens to assess phosphorylation site functionality in high throughput. Nat Methods 2024:10.1038/s41592-024-02256-z. [PMID: 38684783 DOI: 10.1038/s41592-024-02256-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 03/20/2024] [Indexed: 05/02/2024]
Abstract
Signaling pathways that drive gene expression are typically depicted as having a dozen or so landmark phosphorylation and transcriptional events. In reality, thousands of dynamic post-translational modifications (PTMs) orchestrate nearly every cellular function, and we lack technologies to find causal links between these vast biochemical pathways and genetic circuits at scale. Here we describe the high-throughput, functional assessment of phosphorylation sites through the development of PTM-centric base editing coupled to phenotypic screens, directed by temporally resolved phosphoproteomics. Using T cell activation as a model, we observe hundreds of unstudied phosphorylation sites that modulate NFAT transcriptional activity. We identify the phosphorylation-mediated nuclear localization of PHLPP1, which promotes NFAT but inhibits NFκB activity. We also find that specific phosphosite mutants can alter gene expression in subtle yet distinct patterns, demonstrating the potential for fine-tuning transcriptional responses. Overall, base editor screening of PTM sites provides a powerful platform to dissect PTM function within signaling pathways.
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Affiliation(s)
- Patrick H Kennedy
- Laboratory for Immunochemical Circuits, La Jolla Institute for Immunology, La Jolla, CA, USA
- Center of Autoimmunity and Inflammation, La Jolla Institute for Immunology, La Jolla, CA, USA
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Amin Alborzian Deh Sheikh
- Laboratory for Immunochemical Circuits, La Jolla Institute for Immunology, La Jolla, CA, USA
- Center of Autoimmunity and Inflammation, La Jolla Institute for Immunology, La Jolla, CA, USA
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA, USA
| | | | - Alexander C Jones
- Department of Pharmacology, University of California San Diego, San Diego, CA, USA
- Biomedical Sciences Graduate Program, University of California San Diego, San Diego, CA, USA
| | | | - Mudra Hegde
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Maria I Matias
- Laboratory for Immunochemical Circuits, La Jolla Institute for Immunology, La Jolla, CA, USA
- Center of Autoimmunity and Inflammation, La Jolla Institute for Immunology, La Jolla, CA, USA
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Natan Pirete
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Rajan Burt
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jonathan Levy
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Tamia Little
- Laboratory for Immunochemical Circuits, La Jolla Institute for Immunology, La Jolla, CA, USA
- Center of Autoimmunity and Inflammation, La Jolla Institute for Immunology, La Jolla, CA, USA
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Patrick G Hogan
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA, USA
- Program in Immunology, University of California San Diego, San Diego, CA, USA
- Moores Cancer Center, University of California San Diego Health, La Jolla, CA, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - John G Doench
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alexandra C Newton
- Department of Pharmacology, University of California San Diego, San Diego, CA, USA
| | - Rachel A Gottschalk
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Carl G de Boer
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada
| | - Suzie Alarcón
- La Jolla Institute for Immunology, La Jolla, CA, USA
- AUGenomics, San Diego, CA, USA
| | - Gregory A Newby
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Samuel A Myers
- Laboratory for Immunochemical Circuits, La Jolla Institute for Immunology, La Jolla, CA, USA.
- Center of Autoimmunity and Inflammation, La Jolla Institute for Immunology, La Jolla, CA, USA.
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA, USA.
- Department of Pharmacology, University of California San Diego, San Diego, CA, USA.
- Program in Immunology, University of California San Diego, San Diego, CA, USA.
- Moores Cancer Center, University of California San Diego Health, La Jolla, CA, USA.
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2
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Su Q, Zhang J, Lin W, Zhang JF, Newton AC, Mehta S, Yang J, Zhang J. Sensitive Fluorescent Biosensor Reveals Differential Subcellular Regulation of PKC. bioRxiv 2024:2024.03.29.587373. [PMID: 38586003 PMCID: PMC10996667 DOI: 10.1101/2024.03.29.587373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
The protein kinase C (PKC) family of serine/threonine kinases, which consist of three distinctly regulated subfamilies, have long been established as critical for a variety of cellular functions. However, how PKC enzymes are regulated at different subcellular locations, particularly at emerging signaling hubs such as the ER, lysosome, and Par signaling complexes, is unclear. Here, we present a sensitive Excitation Ratiometric (ExRai) C Kinase Activity Reporter (ExRai-CKAR2) that enables the detection of minute changes in subcellular PKC activity. Using ExRai-CKAR2 in conjunction with an enhanced diacylglycerol (DAG) biosensor capable of detecting intracellular DAG dynamics, we uncover the differential regulation of PKC isoforms at distinct subcellular locations. We find that G-protein coupled receptor (GPCR) stimulation triggers sustained PKC activity at the ER and lysosomes, primarily mediated by Ca2+ sensitive conventional PKC (cPKC) and novel PKC (nPKC), respectively, with nPKC showing high basal activity due to elevated basal DAG levels on lysosome membranes. The high sensitivity of ExRai-CKAR2, targeted to either the cytosol or Par-complexes, further enabled us to detect previously inaccessible endogenous atypical PKC (aPKC) activity in 3D organoids. Taken together, ExRai-CKAR2 is a powerful tool for interrogating PKC regulation in response to physiological stimuli.
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Affiliation(s)
- Qi Su
- Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Jing Zhang
- Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Wei Lin
- Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Jin-Fan Zhang
- Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Alexandra C Newton
- Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Sohum Mehta
- Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Jing Yang
- Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Jin Zhang
- Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
- Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
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3
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Patten V, Fischer E, Penndorf P, Newton AC. Tatenda Murigo: A passionate advocate for science in Africa (June 17, 2000-July 14, 2023). IUBMB Life 2024; 76:101-102. [PMID: 37665169 DOI: 10.1002/iub.2781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 08/02/2023] [Indexed: 09/05/2023]
Affiliation(s)
| | | | - Patrick Penndorf
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Alexandra C Newton
- Department of Pharmacology, University of California San Diego, La Jolla, California, USA
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4
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Kennedy PH, Deh Sheikh AA, Balakar M, Jones AC, Olive ME, Hegde M, Matias MI, Pirete N, Burt R, Levy J, Little T, Hogan PG, Liu DR, Doench JG, Newton AC, Gottschalk RA, de Boer C, Alarcón S, Newby G, Myers SA. Proteome-wide base editor screens to assess phosphorylation site functionality in high-throughput. bioRxiv 2023:2023.11.11.566649. [PMID: 38014346 PMCID: PMC10680671 DOI: 10.1101/2023.11.11.566649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Signaling pathways that drive gene expression are typically depicted as having a dozen or so landmark phosphorylation and transcriptional events. In reality, thousands of dynamic post-translational modifications (PTMs) orchestrate nearly every cellular function, and we lack technologies to find causal links between these vast biochemical pathways and genetic circuits at scale. Here, we describe "signaling-to-transcription network" mapping through the development of PTM-centric base editing coupled to phenotypic screens, directed by temporally-resolved phosphoproteomics. Using T cell activation as a model, we observe hundreds of unstudied phosphorylation sites that modulate NFAT transcriptional activity. We identify the phosphorylation-mediated nuclear localization of the phosphatase PHLPP1 which promotes NFAT but inhibits NFκB activity. We also find that specific phosphosite mutants can alter gene expression in subtle yet distinct patterns, demonstrating the potential for fine-tuning transcriptional responses. Overall, base editor screening of PTM sites provides a powerful platform to dissect PTM function within signaling pathways.
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5
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Jung HY, Fattet L, Tsai JH, Kajimoto T, Chang Q, Newton AC, Yang J. Author Correction: Apical-basal polarity inhibits epithelial-mesenchymal transition and tumour metastasis by PAR-complex-mediated SNAI1 degradation. Nat Cell Biol 2023; 25:1385. [PMID: 37580389 DOI: 10.1038/s41556-023-01223-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2023]
Affiliation(s)
- Hae-Yun Jung
- Department of Pharmacology, Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Laurent Fattet
- Department of Pharmacology, Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Jeff H Tsai
- Department of Pharmacology, Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Taketoshi Kajimoto
- Department of Pharmacology, Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Qiang Chang
- Department of Medical Genetics and Department of Neurology, Waisman Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Alexandra C Newton
- Department of Pharmacology, Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Jing Yang
- Department of Pharmacology, Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA.
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.
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6
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Jones AC, Kornev AP, Weng JH, Manning G, Taylor SS, Newton AC. Single-residue mutation in protein kinase C toggles between cancer and neurodegeneration. Biochem J 2023; 480:1299-1316. [PMID: 37551632 PMCID: PMC10586763 DOI: 10.1042/bcj20220397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 08/04/2023] [Accepted: 08/07/2023] [Indexed: 08/09/2023]
Abstract
Conventional protein kinase C (cPKC) isozymes tune the signaling output of cells, with loss-of-function somatic mutations associated with cancer and gain-of-function germline mutations identified in neurodegeneration. PKC with impaired autoinhibition is removed from the cell by quality-control mechanisms to prevent the accumulation of aberrantly active enzyme. Here, we examine how a highly conserved residue in the C1A domain of cPKC isozymes permits quality-control degradation when mutated to histidine in cancer (PKCβ-R42H) and blocks down-regulation when mutated to proline in the neurodegenerative disease spinocerebellar ataxia (PKCγ-R41P). Using FRET-based biosensors, we determined that mutation of R42 to any residue, including lysine, resulted in reduced autoinhibition as indicated by higher basal activity and faster agonist-induced plasma membrane translocation. R42 is predicted to form a stabilizing salt bridge with E655 in the C-tail and mutation of E655, but not neighboring E657, also reduced autoinhibition. Western blot analysis revealed that whereas R42H had reduced stability, the R42P mutant was stable and insensitive to activator-induced ubiquitination and down-regulation, an effect previously observed by deletion of the entire C1A domain. Molecular dynamics (MD) simulations and analysis of stable regions of the domain using local spatial pattern (LSP) alignment suggested that P42 interacts with Q66 to impair mobility and conformation of one of the ligand-binding loops. Additional mutation of Q66 to the smaller asparagine (R42P/Q66N), to remove conformational constraints, restored degradation sensitivity. Our results unveil how disease-associated mutations of the same residue in the C1A domain can toggle between gain- or loss-of-function of PKC.
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Affiliation(s)
- Alexander C. Jones
- Department of Pharmacology, University of California, La Jolla, CA 92093, U.S.A
- Biomedical Sciences Graduate Program, University of California, La Jolla, CA 92093, U.S.A
| | - Alexandr P. Kornev
- Department of Pharmacology, University of California, La Jolla, CA 92093, U.S.A
| | - Jui-Hung Weng
- Department of Pharmacology, University of California, La Jolla, CA 92093, U.S.A
| | | | - Susan S. Taylor
- Department of Pharmacology, University of California, La Jolla, CA 92093, U.S.A
| | - Alexandra C. Newton
- Department of Pharmacology, University of California, La Jolla, CA 92093, U.S.A
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7
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Gu L, Zhu Y, Watari K, Lee M, Liu J, Perez S, Thai M, Mayfield JE, Zhang B, Cunha E Rocha K, Li F, Kim LC, Jones AC, Wierzbicki IH, Liu X, Newton AC, Kisseleva T, Lee JH, Ying W, Gonzalez DJ, Saltiel AR, Simon MC, Karin M. Fructose-1,6-bisphosphatase is a nonenzymatic safety valve that curtails AKT activation to prevent insulin hyperresponsiveness. Cell Metab 2023; 35:1009-1021.e9. [PMID: 37084733 PMCID: PMC10430883 DOI: 10.1016/j.cmet.2023.03.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 02/16/2023] [Accepted: 03/30/2023] [Indexed: 04/23/2023]
Abstract
Insulin inhibits gluconeogenesis and stimulates glucose conversion to glycogen and lipids. How these activities are coordinated to prevent hypoglycemia and hepatosteatosis is unclear. Fructose-1,6-bisphosphatase (FBP1) is rate controlling for gluconeogenesis. However, inborn human FBP1 deficiency does not cause hypoglycemia unless accompanied by fasting or starvation, which also trigger paradoxical hepatomegaly, hepatosteatosis, and hyperlipidemia. Hepatocyte FBP1-ablated mice exhibit identical fasting-conditional pathologies along with AKT hyperactivation, whose inhibition reversed hepatomegaly, hepatosteatosis, and hyperlipidemia but not hypoglycemia. Surprisingly, fasting-mediated AKT hyperactivation is insulin dependent. Independently of its catalytic activity, FBP1 prevents insulin hyperresponsiveness by forming a stable complex with AKT, PP2A-C, and aldolase B (ALDOB), which specifically accelerates AKT dephosphorylation. Enhanced by fasting and weakened by elevated insulin, FBP1:PP2A-C:ALDOB:AKT complex formation, which is disrupted by human FBP1 deficiency mutations or a C-terminal FBP1 truncation, prevents insulin-triggered liver pathologies and maintains lipid and glucose homeostasis. Conversely, an FBP1-derived complex disrupting peptide reverses diet-induced insulin resistance.
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Affiliation(s)
- Li Gu
- Laboratory of Gene Regulation and Signal Transduction, Departments of Pharmacology and Pathology, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Yahui Zhu
- School of Medicine, Chongqing University, Chongqing 400030, China
| | - Kosuke Watari
- Laboratory of Gene Regulation and Signal Transduction, Departments of Pharmacology and Pathology, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Maiya Lee
- Laboratory of Gene Regulation and Signal Transduction, Departments of Pharmacology and Pathology, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Junlai Liu
- Laboratory of Gene Regulation and Signal Transduction, Departments of Pharmacology and Pathology, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sofia Perez
- Laboratory of Gene Regulation and Signal Transduction, Departments of Pharmacology and Pathology, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Melinda Thai
- Laboratory of Gene Regulation and Signal Transduction, Departments of Pharmacology and Pathology, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Joshua E Mayfield
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Bichen Zhang
- Division of Endocrinology & Metabolism, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Karina Cunha E Rocha
- Division of Endocrinology & Metabolism, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Fuming Li
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai 200438, China
| | - Laura C Kim
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alexander C Jones
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Igor H Wierzbicki
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Xiao Liu
- Division of Endocrinology & Metabolism, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Surgery, University of California, San Diego, La Jolla, CA 92093, USA
| | - Alexandra C Newton
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Tatiana Kisseleva
- Department of Surgery, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jun Hee Lee
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Wei Ying
- Division of Endocrinology & Metabolism, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - David J Gonzalez
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Alan R Saltiel
- Division of Endocrinology & Metabolism, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - M Celeste Simon
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael Karin
- Laboratory of Gene Regulation and Signal Transduction, Departments of Pharmacology and Pathology, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
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8
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Jones AC, Kornev AP, Weng JH, Manning G, Taylor SS, Newton AC. Single-residue mutation in protein kinase C toggles between cancer and neurodegeneration. bioRxiv 2023:2023.03.16.532226. [PMID: 36993163 PMCID: PMC10055082 DOI: 10.1101/2023.03.16.532226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Conventional protein kinase C (PKC) isozymes tune the signaling output of cells, with loss-of-function somatic mutations associated with cancer and gain-of-function germline mutations identified in neurodegeneration. PKC with impaired autoinhibition is removed from the cell by quality-control mechanisms to prevent accumulation of aberrantly active enzyme. Here, we examine how a single residue in the C1A domain of PKCβ, arginine 42 (R42), permits quality-control degradation when mutated to histidine in cancer (R42H) and blocks downregulation when mutated to proline in the neurodegenerative disease spinocerebellar ataxia (R42P). Using FRET-based biosensors, we determined that mutation of R42 to any residue, including lysine, resulted in reduced autoinhibition as indicated by higher basal activity and faster agonist-induced plasma membrane translocation. R42 is predicted to form a stabilizing salt bridge with E655 in the C-tail and mutation of E655, but not neighboring E657, also reduced autoinhibition. Western blot analysis revealed that whereas R42H had reduced stability, the R42P mutant was stable and insensitive to activator-induced ubiquitination and downregulation, an effect previously observed by deletion of the entire C1A domain. Molecular dynamics (MD) simulations and analysis of stable regions of the domain using local spatial pattern (LSP) alignment suggested that P42 interacts with Q66 to impair mobility and conformation of one of the ligand-binding loops. Additional mutation of Q66 to the smaller asparagine (R42P/Q66N), to remove conformational constraints, restored degradation sensitivity to that of WT. Our results unveil how disease-associated mutations of the same residue in the C1A domain can toggle between gain- or loss-of-function of PKC.
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9
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Newton AC, Alessi DR. Preface to IUBMB life special issue on protein phosphorylation dedicated to Eddy Fischer. IUBMB Life 2023; 75:282-283. [PMID: 36905647 DOI: 10.1002/iub.2715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 02/21/2023] [Indexed: 03/13/2023]
Affiliation(s)
- Alexandra C Newton
- Department of Pharmacology, University of California San Diego, La Jolla, California, USA
| | - Dario R Alessi
- MRC Protein Phosphorylation and Ubiquitylation Units, University of Dundee, Dundee, Scotland
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10
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Pilo CA, Baffi TR, Kornev AP, Kunkel MT, Malfavon M, Chen DH, Rossitto LA, Chen DX, Huang LC, Longman C, Kannan N, Raskind WH, Gonzalez DJ, Taylor SS, Gorrie G, Newton AC. Mutations in protein kinase Cγ promote spinocerebellar ataxia type 14 by impairing kinase autoinhibition. Sci Signal 2022; 15:eabk1147. [PMID: 36166510 PMCID: PMC9810342 DOI: 10.1126/scisignal.abk1147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Spinocerebellar ataxia type 14 (SCA14) is a neurodegenerative disease caused by germline variants in the diacylglycerol (DAG)/Ca2+-regulated protein kinase Cγ (PKCγ), leading to Purkinje cell degeneration and progressive cerebellar dysfunction. Most of the identified mutations cluster in the DAG-sensing C1 domains. Here, we found with a FRET-based activity reporter that SCA14-associated PKCγ mutations, including a previously undescribed variant, D115Y, enhanced the basal activity of the kinase by compromising its autoinhibition. Unlike other mutations in PKC that impair its autoinhibition but lead to its degradation, the C1 domain mutations protected PKCγ from such down-regulation. This enhanced basal signaling rewired the brain phosphoproteome, as revealed by phosphoproteomic analysis of cerebella from mice expressing a human SCA14-associated H101Y mutant PKCγ transgene. Mutations that induced a high basal activity in vitro were associated with earlier average age of onset in patients. Furthermore, the extent of disrupted autoinhibition, but not agonist-stimulated activity, correlated with disease severity. Molecular modeling indicated that almost all SCA14 variants not within the C1 domain were located at interfaces with the C1B domain, suggesting that mutations in and proximal to the C1B domain are a susceptibility for SCA14 because they uniquely enhance PKCγ basal activity while protecting the enzyme from down-regulation. These results provide insight into how PKCγ activation is modulated and how deregulation of the cerebellar phosphoproteome by SCA14-associated mutations affects disease progression.
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Affiliation(s)
- Caila A. Pilo
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92037, USA
- Biomedical Sciences Graduate Program, University of California, La Jolla, CA 92037, USA
| | - Timothy R. Baffi
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92037, USA
| | - Alexandr P. Kornev
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92037, USA
| | - Maya T. Kunkel
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92037, USA
| | - Mario Malfavon
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92037, USA
| | - Dong-Hui Chen
- Department of Neurology, University of Washington Seattle, WA 98195, USA
| | - Leigh-Ana Rossitto
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92037, USA
- Biomedical Sciences Graduate Program, University of California, La Jolla, CA 92037, USA
| | - Daniel X. Chen
- Department of Neurology, University of Washington Seattle, WA 98195, USA
| | - Liang-Chin Huang
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Cheryl Longman
- Queen Elizabeth University Hospital, Glasgow, Scotland G51 4TF, United Kingdom
| | - Natarajan Kannan
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Wendy H. Raskind
- Department of Medicine/Medical Genetics, University of Washington Seattle, WA 98195, USA
- Department of Psychiatry and Behavioral Sciences, University of Washington Seattle, WA 98195, USA
- Mental Illness Research, Education and Clinical Center, Department of Veterans Affairs, Seattle, WA 98108, USA
| | - David J. Gonzalez
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92037, USA
| | - Susan S. Taylor
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92037, USA
| | - George Gorrie
- Queen Elizabeth University Hospital, Glasgow, Scotland G51 4TF, United Kingdom
| | - Alexandra C. Newton
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92037, USA
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11
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Pilo CA, Newton AC. Two Sides of the Same Coin: Protein Kinase C γ in Cancer and Neurodegeneration. Front Cell Dev Biol 2022; 10:929510. [PMID: 35800893 PMCID: PMC9253466 DOI: 10.3389/fcell.2022.929510] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 05/23/2022] [Indexed: 12/23/2022] Open
Abstract
Protein kinase C (PKC) isozymes transduce myriad signals within the cell in response to the generation of second messengers from membrane phospholipids. The conventional isozyme PKCγ reversibly binds Ca2+ and diacylglycerol, which leads to an open, active conformation. PKCγ expression is typically restricted to neurons, but evidence for its expression in certain cancers has emerged. PKC isozymes have been labeled as oncogenes since the discovery that they bind tumor-promoting phorbol esters, however, studies of cancer-associated PKC mutations and clinical trial data showing that PKC inhibitors have worsened patient survival have reframed PKC as a tumor suppressor. Aberrant expression of PKCγ in certain cancers suggests a role outside the brain, although whether PKCγ also acts as a tumor suppressor remains to be established. On the other hand, PKCγ variants associated with spinocerebellar ataxia type 14 (SCA14), a neurodegenerative disorder characterized by Purkinje cell degeneration, enhance basal activity while preventing phorbol ester-mediated degradation. Although the basis for SCA14 Purkinje cell degeneration remains unknown, studies have revealed how altered PKCγ activity rewires cerebellar signaling to drive SCA14. Importantly, enhanced basal activity of SCA14-associated mutants inversely correlates with age of onset, supporting that enhanced PKCγ activity drives SCA14. Thus, PKCγ activity should likely be inhibited in SCA14, whereas restoring PKC activity should be the goal in cancer therapies. This review describes how PKCγ activity can be lost or gained in disease and the overarching need for a PKC structure as a powerful tool to predict the effect of PKCγ mutations in disease.
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Affiliation(s)
- Caila A. Pilo
- Department of Pharmacology, University of California, San Diego, San Diego, CA, United States
- Biomedical Sciences Graduate Program, University of California, San Diego, San Diego, CA, United States
| | - Alexandra C. Newton
- Department of Pharmacology, University of California, San Diego, San Diego, CA, United States
- *Correspondence: Alexandra C. Newton,
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12
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Mayfield JE, Newton AC, Dixon JE. Divalent cation driven liquid‐liquid phase separation of disordered acidic proteins. FASEB J 2022. [DOI: 10.1096/fasebj.2022.36.s1.r3785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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13
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Baffi TR, Newton AC. Protein kinase C: release from quarantine by mTORC2. Trends Biochem Sci 2022; 47:518-530. [DOI: 10.1016/j.tibs.2022.03.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 02/14/2022] [Accepted: 03/02/2022] [Indexed: 01/31/2023]
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14
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Shedden A, Dunn JC, Martínez-Mota R, Cristóbal-Azkárate J, Gillingham PK, MacSwiney-González C, Newton AC, Rodríguez-Luna E, Korstjens AH. Forest maturity has a stronger influence on the prevalence of spider monkeys than howler monkeys in an anthropogenically impacted rainforest landscape. Primates 2022; 63:283-291. [PMID: 35218456 PMCID: PMC9061665 DOI: 10.1007/s10329-022-00980-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 02/04/2022] [Indexed: 11/29/2022]
Abstract
The transformation and depletion of primary forest over the past few decades have placed almost half of the world’s primate species under the threat of extinction. Developing any successful conservation program for primates requires distribution and demography data, as well as an understanding of the relationships between these factors and their habitat. Between March and June 2010 and 2011 we collected data on the presence and demographic parameters of howler and spider monkeys by carrying out surveys, and validated our findings using local knowledge. We then examined the relationship between forest type and the presence of these primates at 54 sites in the northern area of the Selva Zoque Corridor, Mexico. We detected 86 spider monkey groups across 31 plots and censused 391 individuals (mean ± SD = 5.9 ± 3.0 individuals per sub-group, n = 67 sub-groups). We also detected 69 howler monkey groups across 30 plots and censused 117 individuals (mean ± SD = 5.3 ± 2.4 individuals per group, n = 22 groups). Howler monkey presence was not related to any specific vegetation type, while spider monkeys were present in areas with a higher percentage of tall forest (trees > 25 m high). Overall, spider monkeys were more prevalent than howler monkeys in our sampling sites and showed demographic characteristics similar to those in better protected areas, suggesting that the landscape features in the Uxpanapa Valley are suitable for their needs. Conversely, howler monkey presence was found to be more limited than in other regions, possibly due to the extended presence of spider monkeys.
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Affiliation(s)
- A Shedden
- Faculty of Science and Technology, Bournemouth University, Talbot Campus, Fern Barrow, Poole, BH12 5BB, Dorset, UK.
| | - J C Dunn
- Behavioural Ecology Group, Anglia Ruskin University, Cambridge Campus, East Road, Cambridge, CB1 1PT, UK
- Biological Anthropology, University of Cambridge, Cambridge, CB2 3QG, UK
- Department of Cognitive Biology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - R Martínez-Mota
- Centro de Investigaciones Tropicales, José María Morelos #44, Zona Centro, C.P. 91000, Xalapa, Veracruz, México
| | - J Cristóbal-Azkárate
- Department of Basic Psychological Processes and Their Development, University of the Basque Country, 20018, Donostia-San Sebastián, Spain
| | - P K Gillingham
- Faculty of Science and Technology, Bournemouth University, Talbot Campus, Fern Barrow, Poole, BH12 5BB, Dorset, UK
| | - C MacSwiney-González
- Centro de Investigaciones Tropicales, José María Morelos #44, Zona Centro, C.P. 91000, Xalapa, Veracruz, México
| | - A C Newton
- Faculty of Science and Technology, Bournemouth University, Talbot Campus, Fern Barrow, Poole, BH12 5BB, Dorset, UK
| | - E Rodríguez-Luna
- Centro de Investigaciones Tropicales, José María Morelos #44, Zona Centro, C.P. 91000, Xalapa, Veracruz, México
| | - A H Korstjens
- Faculty of Science and Technology, Bournemouth University, Talbot Campus, Fern Barrow, Poole, BH12 5BB, Dorset, UK
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15
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Abstract
The family of AGC kinases not only regulate cellular biology by phosphorylating substrates, but are themselves controlled by phosphorylation. Phosphorylation generally occurs at two conserved regions in these kinases: a loop near the entrance to the active site, termed the activation loop, that correctly aligns residues for catalysis, and a C-terminal tail whose phosphorylation at a site termed the hydrophobic motif stabilizes the active conformation. Whereas phosphorylation of the activation loop is well established to be catalyzed by the phosphoinositide-dependent kinase 1 (PDK1), the mechanism of phosphorylation of the C-tail hydrophobic motif has been controversial. For a subset of AGC kinases, which includes most protein kinase C (PKC) isozymes and Akt, phosphorylation of the hydrophobic motif in cells was shown to depend on mTORC2 over 15 years ago, yet whether by direct phosphorylation or by another mechanism has remained elusive. The recent identification of a novel and evolutionarily conserved phosphorylation site on the C-tail termed the TOR-Interaction Motif (TIM) has finally unraveled the mystery of how mTORC2 regulates its client kinases. mTORC2 does not directly phosphorylate the hydrophobic motif, rather it converts kinases such as PKC and Akt into a conformation that can ultimately autophosphorylate at the hydrophobic motif. Identification of the direct mTOR phosphorylation that facilitates auto-regulation of the C-tail hydrophobic motif revises the activation mechanisms of mTOR-regulated AGC kinases. This new twist to an old tail opens avenues for therapeutic intervention. Significance Statement The enzyme mTORC2 has been an enigmatic regulator of AGC kinases such as protein kinase C (PKC) and Akt. The recent discovery of a motif named the TOR Interaction Motif in the C-tail of these kinases solves the mystery: mTORC2 marks these kinases for maturity by, ultimately, facilitating autophosphorylation another C-tail site, the hydrophobic motif.
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16
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Baffi TR, Lordén G, Wozniak JM, Feichtner A, Yeung W, Kornev AP, King CC, Del Rio JC, Limaye AJ, Bogomolovas J, Gould CM, Chen J, Kennedy EJ, Kannan N, Gonzalez DJ, Stefan E, Taylor SS, Newton AC. mTORC2 controls the activity of PKC and Akt by phosphorylating a conserved TOR interaction motif. Sci Signal 2021; 14:eabe4509. [PMID: 33850054 PMCID: PMC8208635 DOI: 10.1126/scisignal.abe4509] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The complex mTORC2 is accepted to be the kinase that controls the phosphorylation of the hydrophobic motif, a key regulatory switch for AGC kinases, although whether mTOR directly phosphorylates this motif remains controversial. Here, we identified an mTOR-mediated phosphorylation site that we termed the TOR interaction motif (TIM; F-x3-F-pT), which controls the phosphorylation of the hydrophobic motif of PKC and Akt and the activity of these kinases. The TIM is invariant in mTORC2-dependent AGC kinases, is evolutionarily conserved, and coevolved with mTORC2 components. Mutation of this motif in Akt1 and PKCβII abolished cellular kinase activity by impairing activation loop and hydrophobic motif phosphorylation. mTORC2 directly phosphorylated the PKC TIM in vitro, and this phosphorylation event was detected in mouse brain. Overexpression of PDK1 in mTORC2-deficient cells rescued hydrophobic motif phosphorylation of PKC and Akt by a mechanism dependent on their intrinsic catalytic activity, revealing that mTORC2 facilitates the PDK1 phosphorylation step, which, in turn, enables autophosphorylation. Structural analysis revealed that PKC homodimerization is driven by a TIM-containing helix, and biophysical proximity assays showed that newly synthesized, unphosphorylated PKC dimerizes in cells. Furthermore, disruption of the dimer interface by stapled peptides promoted hydrophobic motif phosphorylation. Our data support a model in which mTORC2 relieves nascent PKC dimerization through TIM phosphorylation, recruiting PDK1 to phosphorylate the activation loop and triggering intramolecular hydrophobic motif autophosphorylation. Identification of TIM phosphorylation and its role in the regulation of PKC provides the basis for AGC kinase regulation by mTORC2.
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Affiliation(s)
- Timothy R Baffi
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA
- Biomedical Sciences Graduate Program, University of California at San Diego, La Jolla, CA 92093, USA
| | - Gema Lordén
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA
| | - Jacob M Wozniak
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA
- Biomedical Sciences Graduate Program, University of California at San Diego, La Jolla, CA 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA 92093, USA
| | - Andreas Feichtner
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innsbruck A-6020, Austria
| | - Wayland Yeung
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Alexandr P Kornev
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA
| | - Charles C King
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA
| | - Jason C Del Rio
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA
- Biomedical Sciences Graduate Program, University of California at San Diego, La Jolla, CA 92093, USA
| | - Ameya J Limaye
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602, USA
| | - Julius Bogomolovas
- Department of Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Christine M Gould
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA
- Biomedical Sciences Graduate Program, University of California at San Diego, La Jolla, CA 92093, USA
| | - Ju Chen
- Department of Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Eileen J Kennedy
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602, USA
| | - Natarajan Kannan
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - David J Gonzalez
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA 92093, USA
| | - Eduard Stefan
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innsbruck A-6020, Austria
| | - Susan S Taylor
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093, USA
| | - Alexandra C Newton
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA.
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17
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Gauron MC, Newton AC, Colombo MI. PKCα Is Recruited to Staphylococcus aureus-Containing Phagosomes and Impairs Bacterial Replication by Inhibition of Autophagy. Front Immunol 2021; 12:662987. [PMID: 33815423 PMCID: PMC8013776 DOI: 10.3389/fimmu.2021.662987] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 03/03/2021] [Indexed: 11/24/2022] Open
Abstract
Hijacking the autophagic machinery is a key mechanism through which invasive pathogens such as Staphylococcus aureus replicate in their host cells. We have previously demonstrated that the bacteria replicate in phagosomes labeled with the autophagic protein LC3, before escaping to the cytoplasm. Here, we show that the Ca2+-dependent PKCα binds to S. aureus-containing phagosomes and that α-hemolysin, secreted by S. aureus, promotes this recruitment of PKCα to phagosomal membranes. Interestingly, the presence of PKCα prevents the association of the autophagic protein LC3. Live cell imaging experiments using the PKC activity reporter CKAR reveal that treatment of cells with S. aureus culture supernatants containing staphylococcal secreted factors transiently activates PKC. Functional studies reveal that overexpression of PKCα causes a marked inhibition of bacterial replication. Taken together, our data identify enhancing PKCα activity as a potential approach to inhibit S. aureus replication in mammalian cells.
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Affiliation(s)
- Maria Celeste Gauron
- Laboratorio de Mecanismos Moleculares Implicados en el Tráfico Vesicular y la Autofagia-Instituto de Histología y Embriología (IHEM)- Universidad Nacional de Cuyo, CONICET- Facultad de Ciencias Médicas, Mendoza, Argentina.,Department of Pharmacology, University of California San Diego, La Jolla, CA, United States
| | - Alexandra C Newton
- Department of Pharmacology, University of California San Diego, La Jolla, CA, United States
| | - María Isabel Colombo
- Laboratorio de Mecanismos Moleculares Implicados en el Tráfico Vesicular y la Autofagia-Instituto de Histología y Embriología (IHEM)- Universidad Nacional de Cuyo, CONICET- Facultad de Ciencias Médicas, Mendoza, Argentina
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18
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Abstract
Whereas protein kinases have been successfully targeted for a variety of diseases, protein phosphatases remain an underutilized therapeutic target, in part because of incomplete characterization of their effects on signaling networks. The pleckstrin homology domain leucine-rich repeat protein phosphatase (PHLPP) is a relatively new player in the cell signaling field, and new roles in controlling the balance among cell survival, proliferation, and apoptosis are being increasingly identified. Originally characterized for its tumor-suppressive function in deactivating the prosurvival kinase Akt, PHLPP may have an opposing role in promoting survival, as recent evidence suggests. Additionally, identification of the transcription factor STAT1 as a substrate unveils a role for PHLPP as a critical mediator of transcriptional programs in cancer and the inflammatory response. This review summarizes the current knowledge of PHLPP as both a tumor suppressor and an oncogene and highlights emerging functions in regulating gene expression and the immune system. Understanding the context-dependent functions of PHLPP is essential for appropriate therapeutic intervention.
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Affiliation(s)
- Timothy R Baffi
- Department of Pharmacology, University of California, San Diego, La Jolla, California 92093-0721, USA;
| | - Ksenya Cohen-Katsenelson
- Department of Pharmacology, University of California, San Diego, La Jolla, California 92093-0721, USA;
| | - Alexandra C Newton
- Department of Pharmacology, University of California, San Diego, La Jolla, California 92093-0721, USA;
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19
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Van AAN, Kunkel MT, Baffi TR, Lordén G, Antal CE, Banerjee S, Newton AC. Protein kinase C fusion proteins are paradoxically loss of function in cancer. J Biol Chem 2021; 296:100445. [PMID: 33617877 PMCID: PMC8008189 DOI: 10.1016/j.jbc.2021.100445] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 02/11/2021] [Accepted: 02/18/2021] [Indexed: 12/02/2022] Open
Abstract
Within the AGC kinase superfamily, gene fusions resulting from chromosomal rearrangements have been most frequently described for protein kinase C (PKC), with gene fragments encoding either the C-terminal catalytic domain or the N-terminal regulatory moiety fused to other genes. Kinase fusions that eliminate regulatory domains are typically gain of function and often oncogenic. However, several quality control pathways prevent accumulation of aberrant PKC, suggesting that PKC fusions may paradoxically be loss of function. To explore this topic, we used biochemical, cellular, and genome editing approaches to investigate the function of fusions that retain the portion of the gene encoding either the catalytic domain or regulatory domain of PKC. Overexpression studies revealed that PKC catalytic domain fusions were constitutively active but vulnerable to degradation. Genome editing of endogenous genes to generate a cancer-associated PKC fusion resulted in cells with detectable levels of fusion transcript but no detectable protein. Hence, PKC catalytic domain fusions are paradoxically loss of function as a result of their instability, preventing appreciable accumulation of protein in cells. Overexpression of a PKC regulatory domain fusion suppressed both basal and agonist-induced endogenous PKC activity, acting in a dominant-negative manner by competing for diacylglycerol. For both catalytic and regulatory domain fusions, the PKC component of the fusion proteins mediated the effects of the full-length fusions on the parameters examined, suggesting that the partner protein is dispensable in these contexts. Taken together, our findings reveal that PKC gene fusions are distinct from oncogenic fusions and present a mechanism by which loss of PKC function occurs in cancer.
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Affiliation(s)
- An-Angela N Van
- Department of Pharmacology, University of California at San Diego, La Jolla, California, USA; Biomedical Sciences Graduate Program, University of California at San Diego, La Jolla, California, USA
| | - Maya T Kunkel
- Department of Pharmacology, University of California at San Diego, La Jolla, California, USA
| | - Timothy R Baffi
- Department of Pharmacology, University of California at San Diego, La Jolla, California, USA; Biomedical Sciences Graduate Program, University of California at San Diego, La Jolla, California, USA
| | - Gema Lordén
- Department of Pharmacology, University of California at San Diego, La Jolla, California, USA
| | - Corina E Antal
- Department of Pharmacology, University of California at San Diego, La Jolla, California, USA; Biomedical Sciences Graduate Program, University of California at San Diego, La Jolla, California, USA
| | - Sourav Banerjee
- Department of Pharmacology, University of California at San Diego, La Jolla, California, USA
| | - Alexandra C Newton
- Department of Pharmacology, University of California at San Diego, La Jolla, California, USA.
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20
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O Macaulay J, C Newton A, Wang AHJ. How does the International Union of Biochemistry and Molecular Biology support education and training? Biochem Mol Biol Educ 2021; 49:7-8. [PMID: 33156978 DOI: 10.1002/bmb.21473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 10/08/2020] [Indexed: 06/11/2023]
Affiliation(s)
- Janet O Macaulay
- Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Alexandra C Newton
- Department of Pharmacology, University of California San Diego (UCSD), La Jolla, California, USA
| | - Andrew H-J Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
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21
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Zhou X, Zhong Y, Molinar-Inglis O, Kunkel MT, Chen M, Sun T, Zhang J, Shyy JYJ, Trejo J, Newton AC, Zhang J. Location-specific inhibition of Akt reveals regulation of mTORC1 activity in the nucleus. Nat Commun 2020; 11:6088. [PMID: 33257668 PMCID: PMC7705703 DOI: 10.1038/s41467-020-19937-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 10/27/2020] [Indexed: 12/13/2022] Open
Abstract
The mechanistic target of rapamycin complex 1 (mTORC1) integrates growth, nutrient and energy status cues to control cell growth and metabolism. While mTORC1 activation at the lysosome is well characterized, it is not clear how this complex is regulated at other subcellular locations. Here, we combine location-selective kinase inhibition, live-cell imaging and biochemical assays to probe the regulation of growth factor-induced mTORC1 activity in the nucleus. Using a nuclear targeted Akt Substrate-based Tandem Occupancy Peptide Sponge (Akt-STOPS) that we developed for specific inhibition of Akt, a critical upstream kinase, we show that growth factor-stimulated nuclear mTORC1 activity requires nuclear Akt activity. Further mechanistic dissection suggests that nuclear Akt activity mediates growth factor-induced nuclear translocation of Raptor, a regulatory scaffolding component in mTORC1, and localization of Raptor to the nucleus results in nuclear mTORC1 activity in the absence of growth factor stimulation. Taken together, these results reveal a mode of regulation of mTORC1 that is distinct from its lysosomal activation, which controls mTORC1 activity in the nuclear compartment.
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Affiliation(s)
- Xin Zhou
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Yanghao Zhong
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA
| | | | - Maya T Kunkel
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Mingyuan Chen
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Tengqian Sun
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Jiao Zhang
- Division of Cardiology, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - John Y-J Shyy
- Division of Cardiology, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - JoAnn Trejo
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Alexandra C Newton
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Jin Zhang
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA.
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, CA, USA.
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22
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Jones AC, Taylor SS, Newton AC, Kornev AP. Hypothesis: Unifying model of domain architecture for conventional and novel protein kinase C isozymes. IUBMB Life 2020; 72:2584-2590. [PMID: 33166426 DOI: 10.1002/iub.2401] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/17/2020] [Accepted: 10/17/2020] [Indexed: 12/26/2022]
Abstract
Protein kinase C (PKC) family members are multi-domain proteins whose function is exquisitely tuned by interdomain interactions that control the spatiotemporal dynamics of their signaling. Despite extensive mechanistic studies on this family of enzymes, no structure of a full-length enzyme that includes all domains has been solved. Here, we take into account the biochemical mechanisms that control autoinhibition, the properties of each individual domain, and previous structural studies to propose a unifying model for the general architecture of PKC family members. This model shows how the C2 domains of conventional and novel PKC isozymes, which have different topologies and different positions in the primary structure, can occupy the same position in the tertiary structure of the kinase. This common architecture of conventional and novel PKC isozymes provides a framework for understanding how disease-associated mutations impair PKC function.
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Affiliation(s)
- Alexander C Jones
- Department of Pharmacology, University of California, San Diego, La Jolla, California, USA.,Biomedical Sciences Graduate Program, University of California, La Jolla, California, USA
| | - Susan S Taylor
- Department of Pharmacology, University of California, San Diego, La Jolla, California, USA
| | - Alexandra C Newton
- Department of Pharmacology, University of California, San Diego, La Jolla, California, USA
| | - Alexandr P Kornev
- Department of Pharmacology, University of California, San Diego, La Jolla, California, USA
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23
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Jones AC, Newton AC. Recognition Motif of Protein Kinase C and Protein Phosphatase 2A. FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.05897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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24
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Lorden G, Wosniak JM, Dozier LE, Patrick GN, Gonzalez DJ, Roberts AJ, Newton AC. Amplified Protein Kinase C Signaling in Alzheimer's Disease. FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.06842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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25
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Van AAN, Kunkel MT, Baffi TR, Antal CE, Newton AC. Protein Kinase C Fusions Reveal Another Mechanism for Loss of Protein Kinase C Function in Cancer. FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.05363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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26
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Zhou X, Zhong Y, Kunkel MT, Newton AC, Zhang J. Tracking mTORC1 Activity in the Nucleus: Distinct Regulation Revealed by Locationspecific Inhibition of Akt. FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.04692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Xin Zhou
- University of California San Diego
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27
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Abstract
Small-molecule inhibitors are a key resource in the cell signaling toolbox. However, because of their global distribution in the cell, they cannot provide a refined understanding of signaling at distinct subcellular locations. Bucko and colleagues have designed a novel tool to localize inhibitors to specific protein scaffolds, opening a new avenue to study localized kinase activity.
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Affiliation(s)
- Agnieszka T Kawashima
- Department of Pharmacology, University of California at San Diego, San Diego, CA 92093, USA; Biomedical Sciences Graduate Program, University of California at San Diego, San Diego, CA 92093
| | - Alexandra C Newton
- Department of Pharmacology, University of California at San Diego, San Diego, CA 92093, USA.
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Pilo CA, Kunkel MT, Van AAN, Kobori EK, Longman C, Gorrie G, Taylor SS, Newton AC. Impaired Autoinhibition of Protein Kinase Cγ in Spinocerebellar Ataxia Type 14. FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.04177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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29
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Kajimoto T, Caliman AD, Tobias IS, Okada T, Pilo CA, Van AAN, McCammon JA, Nakamura SI, Newton AC. A new molecular mechanism of evasion of apoptosis revealed by novel C‐kinase activity reporter. FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.03250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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30
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Pilo CA, Kunkel MT, Van AAN, Kobori EK, Kornev AP, Longman C, Gorrie G, Taylor SS, Newton AC. Impaired Autoinhibition of Protein Kinase Cγ in Spinocerebellar Ataxia Type 14. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.2936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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31
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Cohen Katsenelson K, Stender JD, Kawashima AT, Lordén G, Uchiyama S, Nizet V, Glass CK, Newton AC. PHLPP1 counter-regulates STAT1-mediated inflammatory signaling. eLife 2019; 8:e48609. [PMID: 31408005 PMCID: PMC6692130 DOI: 10.7554/elife.48609] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 07/30/2019] [Indexed: 12/16/2022] Open
Abstract
Inflammation is an essential aspect of innate immunity but also contributes to diverse human diseases. Although much is known about the kinases that control inflammatory signaling, less is known about the opposing phosphatases. Here we report that deletion of the gene encoding PH domain Leucine-rich repeat Protein Phosphatase 1 (PHLPP1) protects mice from lethal lipopolysaccharide (LPS) challenge and live Escherichia coli infection. Investigation of PHLPP1 function in macrophages reveals that it controls the magnitude and duration of inflammatory signaling by dephosphorylating the transcription factor STAT1 on Ser727 to inhibit its activity, reduce its promoter residency, and reduce the expression of target genes involved in innate immunity and cytokine signaling. This previously undescribed function of PHLPP1 depends on a bipartite nuclear localization signal in its unique N-terminal extension. Our data support a model in which nuclear PHLPP1 dephosphorylates STAT1 to control the magnitude and duration of inflammatory signaling in macrophages.
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Affiliation(s)
| | - Joshua D Stender
- Department of Cellular and Molecular MedicineUniversity of California, San DiegoSan DiegoUnited States
| | - Agnieszka T Kawashima
- Department of PharmacologyUniversity of California, San DiegoSan DiegoUnited States
- Department of Pharmacology and Biomedical Sciences Graduate ProgramUniversity of California, San DiegoSan DiegoUnited States
| | - Gema Lordén
- Department of PharmacologyUniversity of California, San DiegoSan DiegoUnited States
| | - Satoshi Uchiyama
- Department of PediatricsUniversity of California, San DiegoSan DiegoUnited States
| | - Victor Nizet
- Department of PediatricsUniversity of California, San DiegoSan DiegoUnited States
- Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of California, San DiegoSan DiegoUnited States
| | - Christopher K Glass
- Department of Cellular and Molecular MedicineUniversity of California, San DiegoSan DiegoUnited States
| | - Alexandra C Newton
- Department of PharmacologyUniversity of California, San DiegoSan DiegoUnited States
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32
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Newton AC. Protein kinases in tune. IUBMB Life 2019; 71:670-671. [DOI: 10.1002/iub.2065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 04/26/2019] [Indexed: 11/12/2022]
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33
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Nowak DG, Katsenelson KC, Watrud KE, Chen M, Mathew G, D'Andrea VD, Lee MF, Swamynathan MM, Casanova-Salas I, Jibilian MC, Buckholtz CL, Ambrico AJ, Pan CH, Wilkinson JE, Newton AC, Trotman LC. The PHLPP2 phosphatase is a druggable driver of prostate cancer progression. J Cell Biol 2019; 218:1943-1957. [PMID: 31092557 PMCID: PMC6548123 DOI: 10.1083/jcb.201902048] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 03/21/2019] [Accepted: 03/29/2019] [Indexed: 12/16/2022] Open
Abstract
Nowak et al. show that loss of the AKT-inactivating phosphatase PHLPP2 paradoxically blocks prostate tumor growth and metastasis. PHLPP2, they find, is critical for MYC stability, suggesting that PHLPP2 inhibitors may present a therapeutic opportunity to target MYC. Metastatic prostate cancer commonly presents with targeted, bi-allelic mutations of the PTEN and TP53 tumor suppressor genes. In contrast, however, most candidate tumor suppressors are part of large recurrent hemizygous deletions, such as the common chromosome 16q deletion, which involves the AKT-suppressing phosphatase PHLPP2. Using RapidCaP, a genetically engineered mouse model of Pten/Trp53 mutant metastatic prostate cancer, we found that complete loss of Phlpp2 paradoxically blocks prostate tumor growth and disease progression. Surprisingly, we find that Phlpp2 is essential for supporting Myc, a key driver of lethal prostate cancer. Phlpp2 dephosphorylates threonine-58 of Myc, which renders it a limiting positive regulator of Myc stability. Furthermore, we show that small-molecule inhibitors of PHLPP2 can suppress MYC and kill PTEN mutant cells. Our findings reveal that the frequent hemizygous deletions on chromosome 16q present a druggable vulnerability for targeting MYC protein through PHLPP2 phosphatase inhibitors.
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Affiliation(s)
- Dawid G Nowak
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY .,Division of Hematology and Medical Oncology, Department of Medicine, Meyer Cancer Center, Weill Cornell Medicine, New York, NY
| | | | | | - Muhan Chen
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
| | - Grinu Mathew
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
| | | | - Matthew F Lee
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
| | | | | | - Megan C Jibilian
- Division of Hematology and Medical Oncology, Department of Medicine, Meyer Cancer Center, Weill Cornell Medicine, New York, NY
| | - Caroline L Buckholtz
- Division of Hematology and Medical Oncology, Department of Medicine, Meyer Cancer Center, Weill Cornell Medicine, New York, NY
| | | | - Chun-Hao Pan
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
| | | | - Alexandra C Newton
- Department of Pharmacology, University of California San Diego, La Jolla, CA
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34
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Van AN, Baffi TR, Kunkel MT, Antal CE, Newton AC. Fusion Gene
TANC2‐PRKCA
Reveals Another Mechanism for Loss of Protein Kinase C Function in Cancer. FASEB J 2019. [DOI: 10.1096/fasebj.2019.33.1_supplement.815.14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- An‐Angela N. Van
- Department of PharmacologyUniversity of California, San DiegoLa JollaCA
- Biomedical Sciences Graduate ProgramUniversity of California, San DiegoLa JollaCA
| | - Timothy R. Baffi
- Department of PharmacologyUniversity of California, San DiegoLa JollaCA
- Biomedical Sciences Graduate ProgramUniversity of California, San DiegoLa JollaCA
| | - Maya T. Kunkel
- Department of PharmacologyUniversity of California, San DiegoLa JollaCA
| | - Corina E. Antal
- Department of PharmacologyUniversity of California, San DiegoLa JollaCA
- Biomedical Sciences Graduate ProgramUniversity of California, San DiegoLa JollaCA
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Baffi TR, Van AAN, Zhao W, Mills GB, Newton AC. Protein Kinase C Quality Control by Phosphatase PHLPP1 Unveils Loss-of-Function Mechanism in Cancer. Mol Cell 2019; 74:378-392.e5. [PMID: 30904392 DOI: 10.1016/j.molcel.2019.02.018] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 12/26/2018] [Accepted: 02/12/2019] [Indexed: 02/02/2023]
Abstract
Protein kinase C (PKC) isozymes function as tumor suppressors in increasing contexts. In contrast to oncogenic kinases, whose function is acutely regulated by transient phosphorylation, PKC is constitutively phosphorylated following biosynthesis to yield a stable, autoinhibited enzyme that is reversibly activated by second messengers. Here, we report that the phosphatase PHLPP1 opposes PKC phosphorylation during maturation, leading to the degradation of aberrantly active species that do not become autoinhibited. Cancer-associated hotspot mutations in the pseudosubstrate of PKCβ that impair autoinhibition result in dephosphorylated and unstable enzymes. Protein-level analysis reveals that PKCα is fully phosphorylated at the PHLPP site in over 5,000 patient tumors, with higher PKC levels correlating (1) inversely with PHLPP1 levels and (2) positively with improved survival in pancreatic adenocarcinoma. Thus, PHLPP1 provides a proofreading step that maintains the fidelity of PKC autoinhibition and reveals a prominent loss-of-function mechanism in cancer by suppressing the steady-state levels of PKC.
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Affiliation(s)
- Timothy R Baffi
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA; Biomedical Sciences Graduate Program, University of California at San Diego, La Jolla, CA 92093, USA
| | - An-Angela N Van
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA; Biomedical Sciences Graduate Program, University of California at San Diego, La Jolla, CA 92093, USA
| | - Wei Zhao
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Gordon B Mills
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Alexandra C Newton
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA.
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36
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Jung HY, Fattet L, Tsai JH, Kajimoto T, Chang Q, Newton AC, Yang J. Apical-basal polarity inhibits epithelial-mesenchymal transition and tumour metastasis by PAR-complex-mediated SNAI1 degradation. Nat Cell Biol 2019; 21:359-371. [PMID: 30804505 PMCID: PMC6546105 DOI: 10.1038/s41556-019-0291-8] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 01/21/2019] [Indexed: 01/06/2023]
Abstract
Loss of apical-basal polarity and activation of epithelial-mesenchymal transition (EMT) both contribute to carcinoma progression and metastasis. Here, we report that apical-basal polarity inhibits EMT to suppress metastatic dissemination. Using mouse and human epithelial three-dimensional organoid cultures, we show that the PAR-atypical protein kinase C (aPKC) polarity complex inhibits EMT and invasion by promoting degradation of the SNAIL family protein SNAI1. Under intact apical-basal polarity, aPKC kinases phosphorylate S249 of SNAI1, which leads to protein degradation. Loss of apical-basal polarity prevents aPKC-mediated SNAI1 phosphorylation and stabilizes the SNAI1 protein to promote EMT and invasion. In human breast tumour xenografts, inhibition of the PAR-complex-mediated SNAI1 degradation mechanism promotes tumour invasion and metastasis. Analyses of human breast tissue samples reveal negative correlations between PAR3 and SNAI1 protein levels. Our results demonstrate that apical-basal polarity functions as a critical checkpoint of EMT to precisely control epithelial-mesenchymal plasticity during tumour metastasis.
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Affiliation(s)
- Hae-Yun Jung
- Department of Pharmacology, Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Laurent Fattet
- Department of Pharmacology, Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Jeff H Tsai
- Department of Pharmacology, Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Taketoshi Kajimoto
- Department of Pharmacology, Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Qiang Chang
- Department of Medical Genetics and Department of Neurology, Waisman Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Alexandra C Newton
- Department of Pharmacology, Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Jing Yang
- Department of Pharmacology, Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA.
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.
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Abstract
Protein kinase C (PKC) isozymes belong to a family of Ser/Thr kinases whose activity is governed by reversible release of an autoinhibitory pseudosubstrate. For conventional and novel isozymes, this is effected by binding the lipid second messenger, diacylglycerol, but for atypical PKC isozymes, this is effected by binding protein scaffolds. PKC shot into the limelight following the discovery in the 1980s that the diacylglycerol-sensitive isozymes are "receptors" for the potent tumor-promoting phorbol esters. This set in place a concept that PKC isozymes are oncoproteins. Yet three decades of cancer clinical trials targeting PKC with inhibitors failed and, in some cases, worsened patient outcome. Emerging evidence from cancer-associated mutations and protein expression levels provide a reason: PKC isozymes generally function as tumor suppressors and their activity should be restored, not inhibited, in cancer therapies. And whereas not enough activity is associated with cancer, variants with enhanced activity are associated with degenerative diseases such as Alzheimer's disease. This review describes the tightly controlled mechanisms that ensure PKC activity is perfectly balanced and what happens when these controls are deregulated. PKC isozymes serve as a paradigm for the wisdom of Confucius: "to go beyond is as wrong as to fall short."
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Affiliation(s)
- Alexandra C Newton
- a Department of Pharmacology , University of California at San Diego , La Jolla , CA , USA
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38
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Kajimoto T, Caliman AD, Tobias IS, Okada T, Pilo CA, Van AAN, Andrew McCammon J, Nakamura SI, Newton AC. Activation of atypical protein kinase C by sphingosine 1-phosphate revealed by an aPKC-specific activity reporter. Sci Signal 2019; 12:eaat6662. [PMID: 30600259 PMCID: PMC6657501 DOI: 10.1126/scisignal.aat6662] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Atypical protein kinase C (aPKC) isozymes are unique in the PKC superfamily in that they are not regulated by the lipid second messenger diacylglycerol, which has led to speculation about whether a different second messenger acutely controls their function. Here, using a genetically encoded reporter that we designed, aPKC-specific C kinase activity reporter (aCKAR), we found that the lipid mediator sphingosine 1-phosphate (S1P) promoted the cellular activity of aPKC. Intracellular S1P directly bound to the purified kinase domain of aPKC and relieved autoinhibitory constraints, thereby activating the kinase. In silico studies identified potential binding sites on the kinase domain, one of which was validated biochemically. In HeLa cells, S1P-dependent activation of aPKC suppressed apoptosis. Together, our findings identify a previously undescribed molecular mechanism of aPKC regulation, a molecular target for S1P in cell survival regulation, and a tool to further explore the biochemical and biological functions of aPKC.
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Affiliation(s)
- Taketoshi Kajimoto
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92037, USA.
- Division of Biochemistry, Department of Biochemistry and Molecular Biology, Graduate School of Medicine, Kobe University, Kobe 650-0017, Japan
| | - Alisha D Caliman
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92037, USA
| | - Irene S Tobias
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92037, USA
| | - Taro Okada
- Division of Biochemistry, Department of Biochemistry and Molecular Biology, Graduate School of Medicine, Kobe University, Kobe 650-0017, Japan
| | - Caila A Pilo
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92037, USA
| | - An-Angela N Van
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92037, USA
| | - J Andrew McCammon
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92037, USA
| | - Shun-Ichi Nakamura
- Division of Biochemistry, Department of Biochemistry and Molecular Biology, Graduate School of Medicine, Kobe University, Kobe 650-0017, Japan
| | - Alexandra C Newton
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92037, USA.
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39
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Balasuriya N, Kunkel MT, Liu X, Biggar KK, Li SSC, Newton AC, O'Donoghue P. Genetic code expansion and live cell imaging reveal that Thr-308 phosphorylation is irreplaceable and sufficient for Akt1 activity. J Biol Chem 2018; 293:10744-10756. [PMID: 29773654 DOI: 10.1074/jbc.ra118.002357] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Revised: 05/08/2018] [Indexed: 01/05/2023] Open
Abstract
The proto-oncogene Akt/protein kinase B (PKB) is a pivotal signal transducer for growth and survival. Growth factor stimulation leads to Akt phosphorylation at two regulatory sites (Thr-308 and Ser-473), acutely activating Akt signaling. Delineating the exact role of each regulatory site is, however, technically challenging and has remained elusive. Here, we used genetic code expansion to produce site-specifically phosphorylated Akt1 to dissect the contribution of each regulatory site to Akt1 activity. We achieved recombinant production of full-length Akt1 containing site-specific pThr and pSer residues for the first time. Our analysis of Akt1 site-specifically phosphorylated at either or both sites revealed that phosphorylation at both sites increases the apparent catalytic rate 1500-fold relative to unphosphorylated Akt1, an increase attributable primarily to phosphorylation at Thr-308. Live imaging of COS-7 cells confirmed that phosphorylation of Thr-308, but not Ser-473, is required for cellular activation of Akt. We found in vitro and in the cell that pThr-308 function cannot be mimicked with acidic residues, nor could unphosphorylated Thr-308 be mimicked by an Ala mutation. An Akt1 variant with pSer-308 achieved only partial enzymatic and cellular signaling activity, revealing a critical interaction between the γ-methyl group of pThr-308 and Cys-310 in the Akt1 active site. Thus, pThr-308 is necessary and sufficient to stimulate Akt signaling in cells, and the common use of phosphomimetics is not appropriate for studying the biology of Akt signaling. Our data also indicate that pThr-308 should be regarded as the primary diagnostic marker of Akt activity.
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Affiliation(s)
| | - Maya T Kunkel
- the Department of Pharmacology, University of California, San Diego, La Jolla, California 92093
| | | | | | | | - Alexandra C Newton
- the Department of Pharmacology, University of California, San Diego, La Jolla, California 92093
| | - Patrick O'Donoghue
- From the Departments of Biochemistry and .,Chemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada and
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40
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Huang LC, Ross KE, Baffi TR, Drabkin H, Kochut KJ, Ruan Z, D'Eustachio P, McSkimming D, Arighi C, Chen C, Natale DA, Smith C, Gaudet P, Newton AC, Wu C, Kannan N. Integrative annotation and knowledge discovery of kinase post-translational modifications and cancer-associated mutations through federated protein ontologies and resources. Sci Rep 2018; 8:6518. [PMID: 29695735 PMCID: PMC5916945 DOI: 10.1038/s41598-018-24457-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 03/23/2018] [Indexed: 11/09/2022] Open
Abstract
Many bioinformatics resources with unique perspectives on the protein landscape are currently available. However, generating new knowledge from these resources requires interoperable workflows that support cross-resource queries. In this study, we employ federated queries linking information from the Protein Kinase Ontology, iPTMnet, Protein Ontology, neXtProt, and the Mouse Genome Informatics to identify key knowledge gaps in the functional coverage of the human kinome and prioritize understudied kinases, cancer variants and post-translational modifications (PTMs) for functional studies. We identify 32 functional domains enriched in cancer variants and PTMs and generate mechanistic hypotheses on overlapping variant and PTM sites by aggregating information at the residue, protein, pathway and species level from these resources. We experimentally test the hypothesis that S768 phosphorylation in the C-helix of EGFR is inhibitory by showing that oncogenic variants altering S768 phosphorylation increase basal EGFR activity. In contrast, oncogenic variants altering conserved phosphorylation sites in the ‘hydrophobic motif’ of PKCβII (S660F and S660C) are loss-of-function in that they reduce kinase activity and enhance membrane translocation. Our studies provide a framework for integrative, consistent, and reproducible annotation of the cancer kinomes.
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Affiliation(s)
- Liang-Chin Huang
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
| | - Karen E Ross
- Protein Information Resource (PIR), Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC, 20007, USA
| | - Timothy R Baffi
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, 92093, USA
| | | | - Krzysztof J Kochut
- Department of Computer Science, University of Georgia, Athens, GA, 30602, USA
| | - Zheng Ruan
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
| | - Peter D'Eustachio
- Department of Biochemistry & Molecular Pharmacology, NYU School of Medicine, New York, NY, 10016, USA
| | - Daniel McSkimming
- Genome, Environment, and Microbiome (GEM) Center of Excellence, University at Buffalo, Buffalo, NY, 14203, USA
| | - Cecilia Arighi
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19711, USA
| | - Chuming Chen
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19711, USA
| | - Darren A Natale
- Protein Information Resource (PIR), Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC, 20007, USA
| | | | - Pascale Gaudet
- SIB Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland
| | - Alexandra C Newton
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Cathy Wu
- Protein Information Resource (PIR), Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC, 20007, USA.,Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19711, USA
| | - Natarajan Kannan
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA.
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41
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Van AN, Baffi TR, Kunkel MT, Antal CE, Newton AC. Cancer‐Associated Fusions of the Protein Kinase C Kinase Domain are Loss‐of‐Function. FASEB J 2018. [DOI: 10.1096/fasebj.2018.32.1_supplement.687.6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- An‐Angela N. Van
- PharmacologyU.C. San DiegoLa JollaCA
- Biomedical Sciences Graduate ProgramU.C. San DiegoLa JollaCA
| | - Timothy R. Baffi
- PharmacologyU.C. San DiegoLa JollaCA
- Biomedical Sciences Graduate ProgramU.C. San DiegoLa JollaCA
| | | | - Corina E. Antal
- PharmacologyU.C. San DiegoLa JollaCA
- Biomedical Sciences Graduate ProgramU.C. San DiegoLa JollaCA
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42
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GRZECHNIK AGNIESZKAT, Wong C, King CC, Gingras A, Newton AC. CDK1‐dependent Phosphorylation of the Tumor Suppressor Phosphatase, PHLPP1, Regulates the Mitotic PHLPP1 Interactome. FASEB J 2018. [DOI: 10.1096/fasebj.2018.32.1_supplement.687.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- AGNIESZKA Teresa GRZECHNIK
- Biomedical Sciences Graduate ProgramUniversity of CaliforniaSan DiegoLa JollaCA
- Department of PharmacologyUniversity of CaliforniaSan DiegoLa JollaCA
| | - Cassandra Wong
- Department of Molecular GeneticsLunenfeld‐Tanenbaum Research Institute Mount Sinai HospitalTorontoONCanada
| | - Charles C. King
- Department of PediatricsUniversity of CaliforniaSan DiegoLa JollaCA
| | - Anne‐Claude Gingras
- Department of Molecular GeneticsLunenfeld‐Tanenbaum Research Institute Mount Sinai HospitalTorontoONCanada
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43
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Baffi TR, Gould CM, Wang Z, Gutkind S, Newton AC. mTORC2 Regulates the Maturation of Protein Kinase C by Folding and Phosphorylation. FASEB J 2018. [DOI: 10.1096/fasebj.2018.32.1_supplement.687.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Timothy R. Baffi
- PharmacologyUniversity of CaliforniaSan DiegoLa JollaCA
- Biomedical Sciences Graduate ProgramLa JollaCA
| | - Christine M. Gould
- PharmacologyUniversity of CaliforniaSan DiegoLa JollaCA
- Biomedical Sciences Graduate ProgramLa JollaCA
| | - Zhiyong Wang
- PharmacologyUniversity of CaliforniaSan DiegoLa JollaCA
- Basic ScienceMoores Cancer CenterLa JollaCA
| | - Silvio Gutkind
- PharmacologyUniversity of CaliforniaSan DiegoLa JollaCA
- Basic ScienceMoores Cancer CenterLa JollaCA
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44
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Kunkel MT, Hudson AM, Brognard J, Newton AC. A Subtle Amino Acid Change Impacts Kinase Function in Dramatically Distinct Ways. FASEB J 2018. [DOI: 10.1096/fasebj.2018.32.1_supplement.662.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Maya T. Kunkel
- Dept. of PharmacologyUniversity of CaliforniaSan DiegoLa JollaCA
| | - Andrew M. Hudson
- Cancer Research UK Manchester InstituteUniversity of ManchesterManchesterUnited Kingdom
| | - John Brognard
- Cancer Research UK Manchester InstituteUniversity of ManchesterManchesterUnited Kingdom
- Center for Cancer ResearchNCIFrederickMD
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Lorden G, Skovsø S, Riopel M, Cohen‐Katsenelson K, Johnson JD, Newton AC. The Protein Phosphatase PHLPP1 Suppresses Insulin Signaling and Inflammation in Mouse Model. FASEB J 2018. [DOI: 10.1096/fasebj.2018.32.1_supplement.670.55] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Gema Lorden
- PharmacologyUniversity of California San DiegoLa JollaCA
| | - Søs Skovsø
- Cellular and Physiological SciencesUniversity of British ColumbiaVancouverBCCanada
| | | | | | - James D. Johnson
- Cellular and Physiological SciencesUniversity of British ColumbiaVancouverBCCanada
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Katsenelson KC, Stender JD, Uchiyama S, Nizet V, Glass CK, Newton AC. The tumor suppressor phosphatase PHLPP1 suppresses inflammatory signaling by regulating the phosphorylation state and activity of STAT1. FASEB J 2018. [DOI: 10.1096/fasebj.2018.32.1_supplement.648.11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Joshua D. Stender
- Cell and Molecular MedicineUniversity of California San DiegoLa JollaCA
| | - Satoshi Uchiyama
- PediatricsSkaggs School of Pharmacy & Pharmaceutical SciencesUniversity of California San DiegoLa JollaCA
| | - Victor Nizet
- PediatricsSkaggs School of Pharmacy & Pharmaceutical SciencesUniversity of California San DiegoLa JollaCA
| | - Chris K. Glass
- Cell and Molecular MedicineUniversity of California San DiegoLa JollaCA
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Kajimoto T, Caliman AD, Tobias IS, Okada T, McCammon JA, Nakamura S, Newton AC. Atypical Protein Kinase C‐specific Activity Reporter Reveals Novel Activation Mechanism of Atypical Protein Kinase C by Sphingosine 1‐phosphate. FASEB J 2018. [DOI: 10.1096/fasebj.2018.32.1_supplement.662.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Taketoshi Kajimoto
- PharmacologyUniversity of California at San DiegoLa JollaCA
- Biochemistry and Molecular BiologyKobe UniversityKobeJapan
| | | | | | - Taro Okada
- Biochemistry and Molecular BiologyKobe UniversityKobeJapan
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Newton AC. Tuning the Signaling Output of Protein Kinase C. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.2970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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Dowling CM, Phelan J, Callender JA, Cathcart MC, Mehigan B, McCormick P, Dalton T, Coffey JC, Newton AC, O'Sullivan J, Kiely PA. Protein kinase C beta II suppresses colorectal cancer by regulating IGF-1 mediated cell survival. Oncotarget 2018; 7:20919-33. [PMID: 26989024 PMCID: PMC4991501 DOI: 10.18632/oncotarget.8062] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 01/31/2016] [Indexed: 12/11/2022] Open
Abstract
Despite extensive efforts, cancer therapies directed at the Protein Kinase C (PKC) family of serine/threonine kinases have failed in clinical trials. These therapies have been directed at inhibiting PKC and have, in some cases, worsened disease outcome. Here we examine colon cancer patients and show not only that PKC Beta II is a tumour suppressor, but patients with low levels of this isozyme have significantly decreased disease free survival. Specifically, analysis of gene expression levels of all PKC genes in matched normal and cancer tissue samples from colon cancer patients revealed a striking down-regulation of the gene coding PKC Beta in the cancer tissue (n = 21). Tissue microarray analysis revealed a dramatic down-regulation of PKC Beta II protein levels in both the epithelial and stromal diseased tissue (n = 166). Of clinical significance, low levels of the protein in the normal tissue of patients is associated with a low (10%) 10 year survival compared with a much higher (60%) survival in patients with relatively high levels of the protein. Consistent with PKC Beta II levels protecting against colon cancer, overexpression of PKC Beta II in colon cancer cell lines reveals that PKC Beta II reverses transformation in cell based assays. Further to this, activation of PKC Beta II results in a dramatic downregulation of IGF-I-induced AKT, indicating a role for PKCs in regulating IGF-1 mediated cell survival. Thus, PKC Beta II is a tumour suppressor in colon cancer and low levels serve as a predictor for poor survival outcome.
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Affiliation(s)
- Catríona M Dowling
- Graduate Entry Medical School and Health Research Institute (HRI), University of Limerick, Limerick, Ireland.,Department of Life Sciences, and Materials and Surface Science Institute, University of Limerick, Limerick, Ireland.,Stokes Research Institute, University of Limerick, Limerick, Ireland
| | - James Phelan
- Department of Surgery, Trinity College Dublin, Dublin, Ireland
| | - Julia A Callender
- Department of Pharmacology, University of California at San Diego, La Jolla, CA, USA
| | | | | | | | - Tara Dalton
- Stokes Research Institute, University of Limerick, Limerick, Ireland
| | - John C Coffey
- 4i Centre for Interventions in Infection, Inflammation and Immunity, Graduate Entry Medical School, University of Limerick, Limerick, Ireland
| | - Alexandra C Newton
- Department of Pharmacology, University of California at San Diego, La Jolla, CA, USA
| | | | - Patrick A Kiely
- Graduate Entry Medical School and Health Research Institute (HRI), University of Limerick, Limerick, Ireland.,Department of Life Sciences, and Materials and Surface Science Institute, University of Limerick, Limerick, Ireland.,Stokes Research Institute, University of Limerick, Limerick, Ireland
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Holland JE, Bennett AE, Newton AC, White PJ, McKenzie BM, George TS, Pakeman RJ, Bailey JS, Fornara DA, Hayes RC. Liming impacts on soils, crops and biodiversity in the UK: A review. Sci Total Environ 2018; 610-611:316-332. [PMID: 28806549 DOI: 10.1016/j.scitotenv.2017.08.020] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 07/14/2017] [Accepted: 08/02/2017] [Indexed: 05/22/2023]
Abstract
Fertile soil is fundamental to our ability to achieve food security, but problems with soil degradation (such as acidification) are exacerbated by poor management. Consequently, there is a need to better understand management approaches that deliver multiple ecosystem services from agricultural land. There is global interest in sustainable soil management including the re-evaluation of existing management practices. Liming is a long established practice to ameliorate acidic soils and many liming-induced changes are well understood. For instance, short-term liming impacts are detected on soil biota and in soil biological processes (such as in N cycling where liming can increase N availability for plant uptake). The impacts of liming on soil carbon storage are variable and strongly relate to soil type, land use, climate and multiple management factors. Liming influences all elements in soils and as such there are numerous simultaneous changes to soil processes which in turn affect the plant nutrient uptake; two examples of positive impact for crops are increased P availability and decreased uptake of toxic heavy metals. Soil physical conditions are at least maintained or improved by liming, but the time taken to detect change varies significantly. Arable crops differ in their sensitivity to soil pH and for most crops there is a positive yield response. Liming also introduces implications for the development of different crop diseases and liming management is adjusted according to crop type within a given rotation. Repeated lime applications tend to improve grassland biomass production, although grassland response is variable and indirect as it relates to changes in nutrient availability. Other indicators of liming response in grassland are detected in mineral content and herbage quality which have implications for livestock-based production systems. Ecological studies have shown positive impacts of liming on biodiversity; such as increased earthworm abundance that provides habitat for wading birds in upland grasslands. Finally, understanding of liming impacts on soil and crop processes are explored together with functional aspects (in terms of ecosystems services) in a new qualitative framework that includes consideration of how liming impacts change with time. This holistic approach provides insights into the far-reaching impacts that liming has on ecosystems and the potential for liming to enhance the multiple benefits from agriculturally managed land. Recommendations are given for future research on the impact of liming and the implications for ecosystem services.
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Affiliation(s)
- J E Holland
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK.
| | - A E Bennett
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - A C Newton
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - P J White
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - B M McKenzie
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - T S George
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - R J Pakeman
- The James Hutton Institute, Craigiebuckler, Aberdeen AB15 8QH, UK
| | - J S Bailey
- Agri-Food and Biosciences Institute, Newforge Lane, Belfast BT9 5PX, UK
| | - D A Fornara
- Agri-Food and Biosciences Institute, Newforge Lane, Belfast BT9 5PX, UK
| | - R C Hayes
- New South Wales Department of Primary Industries, Wagga Wagga Agricultural Institute, Pine Gully Road, Wagga Wagga, NSW 2650, Australia
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