1
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Papaioannou G, Sato T, Houghton C, Kotsalidis PE, Strauss KE, Dean T, Nelson AJ, Stokes M, Gardella TJ, Wein MN. Regulation of intracellular cAMP levels in osteocytes by mechano-sensitive focal adhesion kinase via PDE8A. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.28.601153. [PMID: 38979143 PMCID: PMC11230356 DOI: 10.1101/2024.06.28.601153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Osteocytes are the primary mechano-sensitive cell type in bone. Mechanical loading is sensed across the dendritic projections of osteocytes leading to transient reductions in focal adhesion kinase (FAK) activity. Knowledge regarding the signaling pathways downstream of FAK in osteocytes is incomplete. We performed tyrosine-focused phospho-proteomic profiling in osteocyte-like Ocy454 cells to identify FAK substrates. Gsα, parathyroid hormone receptor (PTH1R), and phosphodiesterase 8A (PDE8A), all proteins associated with cAMP signaling, were found as potential FAK targets based on their reduced tyrosine phosphorylation in both FAK- deficient or FAK inhibitor treated cells. Real time monitoring of intracellular cAMP levels revealed that FAK pharmacologic inhibition or gene deletion increased basal and GPCR ligand-stimulated cAMP levels and downstream phosphorylation of protein kinase A substrates. Mutating FAK phospho-acceptor sites in Gsα and PTH1R had no effect on PTH- or FAK inhibitor-stimulated cAMP levels. Since FAK inhibitor treatment augmented cAMP levels even in the presence of forskolin, we focused on potential FAK substrates downstream of cAMP generation. Indeed, PDE8A inhibition mimicked FAK inhibition at the level of increased cAMP, PKA activity, and expression of cAMP-regulated target genes. In vitro kinase assay showed that PDE8A is directly phosphorylated by FAK while immunoprecipitation assays revealed intracellular association between FAK and PDE8A. Thus, FAK inhibition in osteocytes acts synergistically with signals that activate adenylate cyclase to increase intracellular cAMP. Mechanically-regulated FAK can modulate intracellular cAMP levels via effects on PDE8A. These data suggest a novel signal transduction mechanism that mediates crosstalk between mechanical and cAMP-linked hormonal signaling in osteocytes.
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Mohanty S, Suklabaidya S, Lavorgna A, Ueno T, Fujisawa JI, Ngouth N, Jacobson S, Harhaj EW. The tyrosine kinase KDR is essential for the survival of HTLV-1-infected T cells by stabilizing the Tax oncoprotein. Nat Commun 2024; 15:5380. [PMID: 38918393 PMCID: PMC11199648 DOI: 10.1038/s41467-024-49737-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 06/18/2024] [Indexed: 06/27/2024] Open
Abstract
Human T-cell leukemia virus type 1 (HTLV-1) infection is linked to the development of adult T-cell leukemia/lymphoma (ATLL) and the neuroinflammatory disease, HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP). The HTLV-1 Tax oncoprotein regulates viral gene expression and persistently activates NF-κB to maintain the viability of HTLV-1-infected T cells. Here, we utilize a kinome-wide shRNA screen to identify the tyrosine kinase KDR as an essential survival factor of HTLV-1-transformed cells. Inhibition of KDR specifically induces apoptosis of Tax expressing HTLV-1-transformed cell lines and CD4 + T cells from HAM/TSP patients. Furthermore, inhibition of KDR triggers the autophagic degradation of Tax resulting in impaired NF-κB activation and diminished viral transmission in co-culture assays. Tax induces the expression of KDR, forms a complex with KDR, and is phosphorylated by KDR. These findings suggest that Tax stability is dependent on KDR activity which could be exploited as a strategy to target Tax in HTLV-1-associated diseases.
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Affiliation(s)
- Suchitra Mohanty
- Department of Microbiology and Immunology, Penn State College School of Medicine, Hershey, PA, USA
| | - Sujit Suklabaidya
- Department of Microbiology and Immunology, Penn State College School of Medicine, Hershey, PA, USA
| | - Alfonso Lavorgna
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Millipore-Sigma, Rockville, MD, USA
| | - Takaharu Ueno
- Department of Microbiology, Kansai Medical University, Osaka, Japan
| | | | - Nyater Ngouth
- Viral Immunology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Steven Jacobson
- Viral Immunology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Edward W Harhaj
- Department of Microbiology and Immunology, Penn State College School of Medicine, Hershey, PA, USA.
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3
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Ranjbarvaziri S, Zeng A, Wu I, Greer-Short A, Farshidfar F, Budan A, Xu E, Shenwai R, Kozubov M, Li C, Van Pell M, Grafton F, MacKay CE, Song X, Priest JR, Argast G, Mandegar MA, Hoey T, Yang J. Targeting HDAC6 to treat heart failure with preserved ejection fraction in mice. Nat Commun 2024; 15:1352. [PMID: 38409164 PMCID: PMC10897156 DOI: 10.1038/s41467-024-45440-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 01/22/2024] [Indexed: 02/28/2024] Open
Abstract
Heart failure with preserved ejection fraction (HFpEF) poses therapeutic challenges due to the limited treatment options. Building upon our previous research that demonstrates the efficacy of histone deacetylase 6 (HDAC6) inhibition in a genetic cardiomyopathy model, we investigate HDAC6's role in HFpEF due to their shared mechanisms of inflammation and metabolism. Here, we show that inhibiting HDAC6 with TYA-018 effectively reverses established heart failure and its associated symptoms in male HFpEF mouse models. Additionally, in male mice lacking Hdac6 gene, HFpEF progression is delayed and they are resistant to TYA-018's effects. The efficacy of TYA-018 is comparable to a sodium-glucose cotransporter 2 (SGLT2) inhibitor, and the combination shows enhanced effects. Mechanistically, TYA-018 restores gene expression related to hypertrophy, fibrosis, and mitochondrial energy production in HFpEF heart tissues. Furthermore, TYA-018 also inhibits activation of human cardiac fibroblasts and enhances mitochondrial respiratory capacity in cardiomyocytes. In this work, our findings show that HDAC6 impacts on heart pathophysiology and is a promising target for HFpEF treatment.
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Affiliation(s)
| | - Aliya Zeng
- Tenaya Therapeutics, South San Francisco, CA, USA
| | - Iris Wu
- Tenaya Therapeutics, South San Francisco, CA, USA
| | | | | | - Ana Budan
- Tenaya Therapeutics, South San Francisco, CA, USA
| | - Emma Xu
- Tenaya Therapeutics, South San Francisco, CA, USA
| | - Reva Shenwai
- Tenaya Therapeutics, South San Francisco, CA, USA
| | | | - Cindy Li
- Tenaya Therapeutics, South San Francisco, CA, USA
| | | | | | | | - Xiaomei Song
- Tenaya Therapeutics, South San Francisco, CA, USA
| | | | | | | | - Timothy Hoey
- Tenaya Therapeutics, South San Francisco, CA, USA
| | - Jin Yang
- Tenaya Therapeutics, South San Francisco, CA, USA.
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4
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Grimes KM, Maillet M, Swoboda CO, Bowers SLK, Millay DP, Molkentin JD. MEK1-ERK1/2 signaling regulates the cardiomyocyte non-sarcomeric actin cytoskeletal network. Am J Physiol Heart Circ Physiol 2024; 326:H180-H189. [PMID: 37999644 DOI: 10.1152/ajpheart.00612.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 11/09/2023] [Accepted: 11/15/2023] [Indexed: 11/25/2023]
Abstract
During select pathological conditions, the heart can hypertrophy and remodel in either a dilated or concentric ventricular geometry, which is associated with lengthening or widening of cardiomyocytes, respectively. The mitogen-activated protein kinase kinase 1 (MEK1) and extracellular signal-related kinase 1 and 2 (ERK1/2) pathway has been implicated in these differential types of growth such that cardiac overexpression of activated MEK1 causes profound concentric hypertrophy and cardiomyocyte thickening, while genetic ablation of the genes encoding ERK1/2 in the mouse heart causes dilation and cardiomyocyte lengthening. However, the mechanisms by which this kinase signaling pathway controls cardiomyocyte directional growth as well as its downstream effectors are poorly understood. To investigate this, we conducted an unbiased phosphoproteomic screen in cultured neonatal rat ventricular myocytes treated with an activated MEK1 adenovirus, the MEK1 inhibitor U0126, or an eGFP adenovirus control. Bioinformatic analysis identified cytoskeletal-related proteins as the largest subset of differentially phosphorylated proteins. Phos-tag and traditional Western blotting were performed to confirm that many cytoskeletal proteins displayed changes in phosphorylation with manipulations in MEK1-ERK1/2 signaling. From this, we hypothesized that the actin cytoskeleton would be changed in vivo in the mouse heart. Indeed, we found that activated MEK1 transgenic mice and gene-deleted mice lacking ERK1/2 protein had enhanced non-sarcomeric actin expression in cardiomyocytes compared with wild-type control hearts. Consistent with these results, cytoplasmic β- and γ-actin were increased at the subcortical intracellular regions of adult cardiomyocytes. Together, these data suggest that MEK1-ERK1/2 signaling influences the non-sarcomeric cytoskeletal actin network, which may be important for facilitating the growth of cardiomyocytes in length and/or width.NEW & NOTEWORTHY Here, we performed an unbiased analysis of the total phosphoproteome downstream of MEK1-ERK1/2 kinase signaling in cardiomyocytes. Pathway analysis suggested that proteins of the non-sarcomeric cytoskeleton were the most differentially affected. We showed that cytoplasmic β-actin and γ-actin isoforms, regulated by MEK1-ERK1/2, are localized to the subcortical space at both lateral membranes and intercalated discs of adult cardiomyocytes suggesting how MEK1-ERK1/2 signaling might underlie directional growth of adult cardiomyocytes.
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Affiliation(s)
- Kelly M Grimes
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio, United States
| | - Marjorie Maillet
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio, United States
| | - Casey O Swoboda
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio, United States
| | - Stephanie L K Bowers
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio, United States
| | - Doug P Millay
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio, United States
| | - Jeffery D Molkentin
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio, United States
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5
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Koide E, Mohardt ML, Doctor ZM, Yang A, Hao M, Donovan KA, Kuismi CC, Nelson AJ, Abell K, Aguiar M, Che J, Stokes MP, Zhang T, Aguirre AJ, Fischer ES, Gray NS, Jiang B, Nabet B. Development and Characterization of Selective FAK Inhibitors and PROTACs with In Vivo Activity. Chembiochem 2023; 24:e202300141. [PMID: 37088717 PMCID: PMC10590827 DOI: 10.1002/cbic.202300141] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 04/14/2023] [Accepted: 04/17/2023] [Indexed: 04/25/2023]
Abstract
Focal adhesion kinase (FAK) is an attractive drug target due to its overexpression in cancer. FAK functions as a non-receptor tyrosine kinase and scaffolding protein, coordinating several downstream signaling effectors and cellular processes. While drug discovery efforts have largely focused on targeting FAK kinase activity, FAK inhibitors have failed to show efficacy as single agents in clinical trials. Here, using structure-guided design, we report the development of a selective FAK inhibitor (BSJ-04-175) and degrader (BSJ-04-146) to evaluate the consequences and advantages of abolishing all FAK activity in cancer models. BSJ-04-146 achieves rapid and potent FAK degradation with high proteome-wide specificity in cancer cells and induces durable degradation in mice. Compared to kinase inhibition, targeted degradation of FAK exhibits pronounced improved activity on downstream signaling and cancer cell viability and migration. Together, BSJ-04-175 and BSJ-04-146 are valuable chemical tools to dissect the specific consequences of targeting FAK through small-molecule inhibition or degradation.
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Affiliation(s)
- Eriko Koide
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mikaela L. Mohardt
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Zainab M. Doctor
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Annan Yang
- Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mingfeng Hao
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Katherine A. Donovan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | | | | | | | | | - Jianwei Che
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | | | - Tinghu Zhang
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford Medicine, Stanford University, Stanford, CA, USA
| | - Andrew J. Aguirre
- Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eric S. Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Nathanael S. Gray
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford Medicine, Stanford University, Stanford, CA, USA
| | - Baishan Jiang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Behnam Nabet
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
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6
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Umfress A, Chakraborti A, Priya Sudarsana Devi S, Adams R, Epstein D, Massicano A, Sorace A, Singh S, Iqbal Hossian M, Andrabi SA, Crossman DK, Kumar N, Shahid Mukhtar M, Luo H, Simpson C, Abell K, Stokes M, Wiederhold T, Rosen C, Lu H, Natarajan A, Bibb JA. Cdk5 mediates rotational force-induced brain injury. Sci Rep 2023; 13:3394. [PMID: 36854738 PMCID: PMC9974974 DOI: 10.1038/s41598-023-29322-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 02/02/2023] [Indexed: 03/02/2023] Open
Abstract
Millions of traumatic brain injuries (TBIs) occur annually. TBIs commonly result from falls, traffic accidents, and sports-related injuries, all of which involve rotational acceleration/deceleration of the brain. During these injuries, the brain endures a multitude of primary insults including compression of brain tissue, damaged vasculature, and diffuse axonal injury. All of these deleterious effects can contribute to secondary brain ischemia, cellular death, and neuroinflammation that progress for weeks, months, and lifetime after injury. While the linear effects of head trauma have been extensively modeled, less is known about how rotational injuries mediate neuronal damage following injury. Here, we developed a new model of repetitive rotational head trauma in rodents and demonstrated acute and prolonged pathological, behavioral, and electrophysiological effects of rotational TBI (rTBI). We identify aberrant Cyclin-dependent kinase 5 (Cdk5) activity as a principal mediator of rTBI. We utilized Cdk5-enriched phosphoproteomics to uncover potential downstream mediators of rTBI and show pharmacological inhibition of Cdk5 reduces the cognitive and pathological consequences of injury. These studies contribute meaningfully to our understanding of the mechanisms of rTBI and how they may be effectively treated.
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Affiliation(s)
- Alan Umfress
- Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Ayanabha Chakraborti
- Department of Translational Neuroscience, University of Arizona College of Medicine in Phoeni, Biomedical Sciences Partnership Bldg, Phoenix, AZ, 85004 , USA
| | | | - Raegan Adams
- Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Daniel Epstein
- Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Adriana Massicano
- Department of Radiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Anna Sorace
- Department of Radiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Sarbjit Singh
- Eppley Institute for Research in Cancer and Allied Diseases University of Nebraska Medical Center, Omaha, NE, USA
| | - M Iqbal Hossian
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Shaida A Andrabi
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - David K Crossman
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Nilesh Kumar
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - M Shahid Mukhtar
- Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, USA
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | | | | | | | | | - Charles Rosen
- OSF Healthcare Illinois Neurological Institute, Peoria, IL, USA
| | - Hongbing Lu
- Department of Mechanical Engineering, University of Texas at Dallas, Dallas, TX, USA
| | - Amarnath Natarajan
- Eppley Institute for Research in Cancer and Allied Diseases University of Nebraska Medical Center, Omaha, NE, USA
| | - James A Bibb
- Department of Translational Neuroscience, University of Arizona College of Medicine in Phoeni, Biomedical Sciences Partnership Bldg, Phoenix, AZ, 85004 , USA.
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7
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Henderson IM, Marez C, Dokladny K, Smoake J, Martinez M, Johnson D, Uhl GR. Substrate-selective positive allosteric modulation of PTPRD’s phosphatase by flavonols. Biochem Pharmacol 2022; 202:115109. [PMID: 35636503 PMCID: PMC10184881 DOI: 10.1016/j.bcp.2022.115109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 05/23/2022] [Accepted: 05/23/2022] [Indexed: 11/30/2022]
Abstract
The receptor type protein tyrosine phosphatase D (PTPRD) is expressed by neurons and implicated in interesting phenotypes that include reward from addictive substances, restless leg syndrome and neurofibrillary tangle densities in Alzheimer's disease (AD-NFTs). However, the brain phosphotyrosine phosphoprotein (PTPP) substrates for PTPRD's phosphatase have not been clearly defined. Although we have identified small molecule inhibitors of PTPRD's phosphatase that are candidates for reducing reward from addictive substances, no positive allosteric modulators of this phosphatase that might be candidates for reducing AD-NFTs have been reported. We now report identification of candidate brain substrates for PTPRD based on their increased phosphorylation in knockout vs wildtype animals, coexpression with PTPRD in neuronal subtypes and brisk dephosphorylation by recombinant human PTPRD phosphatase. We also report discovery that quercetin and other flavonols, though not closely-related flavones, enhance rates of PTPRD's dephosphorylation of a group of these candidate substrate PTPPs but not others. This substrate-selective positive allosteric modulation provides a novel pharmacological action. Flavonol-mediated increases in PTPRD's dephosphorylation of the GSK3 β and α kinases that hyperphosphorylate tau, the major component of AD-NFTs, could help to explain recent data concerning genetic and dietary impacts on Alzheimer's disease.
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Affiliation(s)
- Ian M Henderson
- Biomedical Research Institute of New Mexico, Albuquerque, NM 87108, United States; New Mexico VA Healthcare System, Albuquerque, NM 87108, United States
| | - Carlissa Marez
- Biomedical Research Institute of New Mexico, Albuquerque, NM 87108, United States; New Mexico VA Healthcare System, Albuquerque, NM 87108, United States
| | - Karol Dokladny
- Department of Medicine, University of New Mexico, Albuquerque, NM 87131, United States
| | - Jane Smoake
- Biomedical Research Institute of New Mexico, Albuquerque, NM 87108, United States; New Mexico VA Healthcare System, Albuquerque, NM 87108, United States
| | - Maria Martinez
- Biomedical Research Institute of New Mexico, Albuquerque, NM 87108, United States; New Mexico VA Healthcare System, Albuquerque, NM 87108, United States
| | - David Johnson
- College of Pharmacy, University of Kansas, Lawrence, KS 66045, United States
| | - George R Uhl
- Biomedical Research Institute of New Mexico, Albuquerque, NM 87108, United States; New Mexico VA Healthcare System, Albuquerque, NM 87108, United States; Departments of Neurology, Neuroscience and Molecular Genetics and Microbiology, University of New Mexico, Albuquerque, NM 87131, United States; Departments of Neurology and Pharmacology, University of Maryland School of Medicine, Baltimore, MD 21201, United States; Maryland VA Healthcare System, Baltimore, MD 21201, United States.
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8
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Chang M, Huhn S, Nelson L, Betenbaugh M, Du Z. Significant impact of mTORC1 and ATF4 pathways in CHO cell recombinant protein production induced by CDK4/6 inhibitor. Biotechnol Bioeng 2022; 119:1189-1206. [PMID: 35112712 DOI: 10.1002/bit.28050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/03/2022] [Accepted: 01/24/2022] [Indexed: 11/11/2022]
Abstract
The CDK4/6 inhibitor has been shown to increase recombinant protein productivity in Chinese hamster ovary cells (CHO). Therefore, we investigated the mechanism that couples cell cycle inhibitor (CCI) treatment with protein productivity utilizing proteomics and phosphoproteomics. We identified mTORC1 as a critical early signaling event that preceded boosted productivity. Following CCI treatment, mTOR exhibited a transient increase in phosphorylation at a novel site that is also conserved in human and mouse. Upstream of mTORC1, increased phosphorylation of AKT1S1 and decreased phosphorylation of RB1 may provide molecular links between CDK4/6 inhibition and mTORC1. Downstream, increased EIF4EBP phosphorylation was observed, which can mediate cap-dependent translation. In addition, the collective effect of increased phosphorylation of RPS6, increased phosphorylation of regulators of RNA polymerase I, and increased protein expression in tRNA-aminoacylation pathway may contribute to enhancing the translational apparatus for increased productivity. In concert, an elevated stress response via GCN2/EIF2AK4-ATF4 axis persisted over the treatment course, which may link mTOR to downstream responses including the unfolded protein response (UPR) and autophagy to enhance proper protein folding and secretion. Together, this comprehensive proteomics and phosphoproteomics characterization of CCI treated CHO cells offers insights into understanding multiple aspects of signaling events resulting from CDK4/CDK6 inhibition. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Meiping Chang
- Process Cell Sciences, Biologics Process R&D, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Steven Huhn
- Process Cell Sciences, Biologics Process R&D, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Luke Nelson
- Process Cell Sciences, Biologics Process R&D, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Michael Betenbaugh
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Zhimei Du
- Process Cell Sciences, Biologics Process R&D, Merck & Co., Inc., Kenilworth, NJ, USA
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9
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Khbouz B, Rowart P, Poma L, Dahlke E, Bottner M, Stokes M, Bolen G, Rahmouni S, Theilig F, Jouret F. The genetic deletion of the Dual Specificity Phosphatase 3 (DUSP3) attenuates kidney damage and inflammation following ischaemia/reperfusion injury in mouse. Acta Physiol (Oxf) 2022; 234:e13735. [PMID: 34704357 DOI: 10.1111/apha.13735] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 10/20/2021] [Accepted: 10/22/2021] [Indexed: 12/16/2022]
Abstract
AIM Dual Specificity Phosphatase 3 (DUSP3) regulates the innate immune response, with a putative role in angiogenesis. Modulating inflammation and perfusion contributes to renal conditioning against ischaemia/reperfusion (I/R). We postulate that the functional loss of DUSP3 is associated with kidney resistance to I/R. METHODS Ten C57BL/6 male WT and Dusp3-/- mice underwent right nephrectomy and left renal I/R (30 min/48 hours). Renal injury was assessed based on serum levels of urea (BUN) and Jablonski score. The expression of CD31 and VEGF vascular markers was quantified by RT-qPCR and immuno-staining. Renal resistivity index (RRI) was measured in vivo by Doppler ultrasound. Comparative phosphoproteomics was conducted using IMAC enrichment of phosphopeptides. Inflammatory markers were quantified at both mRNA and protein levels in ischaemic vs non-ischaemic kidneys in WT vs Dusp3-/- . RESULTS At baseline, we located DUSP3 in renal glomeruli and endothelial cells. CD31-positive vascular network was significantly larger in Dusp3-/- kidneys compared to WT, with a lower RRI in Dusp3-/- mice. Following I/R, BUN and Jablonski score were significantly lower in Dusp3-/- vs WT mice. Phosphoproteomics highlighted a down-regulation of inflammatory pathways and up-regulation of phospho-sites involved in cell metabolism and VEGF-related angiogenesis in Dusp3-/- vs WT ischaemic kidneys. Dusp3-/- ischaemic kidneys showed decreased mRNA levels of CD11b, TNF-α, KIM-1, IL-6, IL-1β and caspase-3 compared to controls. The numbers of PCNA-, F4-80- and CD11b-positive cells were reduced in Dusp3-/- vs WT kidneys post-I/R. CONCLUSION Genetic inactivation of Dusp3 is associated with kidney conditioning against I/R, possibly due to attenuated inflammation and improved perfusion.
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Affiliation(s)
- Badr Khbouz
- Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA) Cardiovascular Sciences University of Liège (ULiège) Liège Belgium
| | - Pascal Rowart
- Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA) Cardiovascular Sciences University of Liège (ULiège) Liège Belgium
- Department of Pharmacology and Chemical Biology School of Medicine University of Pittsburgh Pittsburgh Pennsylvania USA
| | - Laurence Poma
- Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA) Cardiovascular Sciences University of Liège (ULiège) Liège Belgium
| | - Eileen Dahlke
- Institute of Anatomy Christian Albrechts‐University Kiel Germany
| | - Martina Bottner
- Institute of Anatomy Christian Albrechts‐University Kiel Germany
| | - Matthew Stokes
- Cell Signaling Technology, Inc. Danvers Massachusetts USA
| | - Géraldine Bolen
- Department of Clinical Sciences Fundamental and Applied Research for Animals & Health (FARAH) Veterinary Faculty University of Liège (ULiège) Liège Belgium
| | - Souad Rahmouni
- Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA) Medical Genomics University of Liège (ULiège) Liège Belgium
| | - Franziska Theilig
- Institute of Anatomy Christian Albrechts‐University Kiel Germany
- Institute of Anatomy Department of Medicine University of Fribourg Fribourg Switzerland
| | - François Jouret
- Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA) Cardiovascular Sciences University of Liège (ULiège) Liège Belgium
- Division of Nephrology CHU of Liège University of Liège (CHU ULiège) Liège Belgium
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10
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Tsai CF, Ogata K, Sugiyama N, Ishihama Y. Motif-centric phosphoproteomics to target kinase-mediated signaling pathways. CELL REPORTS METHODS 2022; 2:100138. [PMID: 35474870 PMCID: PMC9017188 DOI: 10.1016/j.crmeth.2021.100138] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 10/08/2021] [Accepted: 12/13/2021] [Indexed: 12/27/2022]
Abstract
Identifying cellular phosphorylation pathways based on kinase-substrate relationships is a critical step to understanding the regulation of physiological functions in cells. Mass spectrometry-based phosphoproteomics workflows have made it possible to comprehensively collect information on individual phosphorylation sites in a variety of samples. However, there is still no generic approach to uncover phosphorylation networks based on kinase-substrate relationships in rare cell populations. Here, we describe a motif-centric phosphoproteomics approach combined with multiplexed isobaric labeling, in which in vitro kinase reactions are used to generate targeted phosphopeptides, which are spiked into one of the isobaric channels to increase detectability. Proof-of-concept experiments demonstrate selective and comprehensive quantification of targeted phosphopeptides by using multiple kinases for motif-centric channels. More than 7,000 tyrosine phosphorylation sites were quantified from several tens of micrograms of starting materials. This approach enables the quantification of multiple phosphorylation pathways under physiological or pathological regulation in a motif-centric manner.
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Affiliation(s)
- Chia-Feng Tsai
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Kosuke Ogata
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Naoyuki Sugiyama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Yasushi Ishihama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
- Laboratory of Clinical and Analytical Chemistry, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, Japan
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11
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Global Proteome Profiling to Assess Changes in Protein Abundance Using Isobaric Labeling and Liquid Chromatography-Tandem Mass Spectrometry. Methods Mol Biol 2021. [PMID: 34432251 DOI: 10.1007/978-1-0716-1665-9_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Protein degradation is a critical component of all facets of cell biology, and recently methods have been developed to make use of targeted protein degradation as both an investigative tool and a potential therapeutic avenue. Mass spectrometry-based proteomic studies have allowed detailed characterization of changes in protein level and the biology underlying growth, development, and disease. Current methods and instrumentation allow identification and quantitative analysis of thousands of proteins in a single assay. The method described here involves cell lysis and digestion to peptides, labeling peptides with isobaric tagging TMT reagents, basic reversed phase fractionation, and liquid chromatography-tandem mass spectrometry analysis of the enriched peptides.
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12
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Mulvaney KM, Blomquist C, Acharya N, Li R, Ranaghan MJ, O'Keefe M, Rodriguez DJ, Young MJ, Kesar D, Pal D, Stokes M, Nelson AJ, Jain SS, Yang A, Mullin-Bernstein Z, Columbus J, Bozal FK, Skepner A, Raymond D, LaRussa S, McKinney DC, Freyzon Y, Baidi Y, Porter D, Aguirre AJ, Ianari A, McMillan B, Sellers WR. Molecular basis for substrate recruitment to the PRMT5 methylosome. Mol Cell 2021; 81:3481-3495.e7. [PMID: 34358446 DOI: 10.1016/j.molcel.2021.07.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 06/07/2021] [Accepted: 07/14/2021] [Indexed: 12/15/2022]
Abstract
PRMT5 is an essential arginine methyltransferase and a therapeutic target in MTAP-null cancers. PRMT5 uses adaptor proteins for substrate recruitment through a previously undefined mechanism. Here, we identify an evolutionarily conserved peptide sequence shared among the three known substrate adaptors (CLNS1A, RIOK1, and COPR5) and show that it is necessary and sufficient for interaction with PRMT5. We demonstrate that PRMT5 uses modular adaptor proteins containing a common binding motif for substrate recruitment, comparable with other enzyme classes such as kinases and E3 ligases. We structurally resolve the interface with PRMT5 and show via genetic perturbation that it is required for methylation of adaptor-recruited substrates including the spliceosome, histones, and ribosomal complexes. Furthermore, disruption of this site affects Sm spliceosome activity, leading to intron retention. Genetic disruption of the PRMT5-substrate adaptor interface impairs growth of MTAP-null tumor cells and is thus a site for development of therapeutic inhibitors of PRMT5.
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Affiliation(s)
| | | | | | | | - Matthew J Ranaghan
- Center for the Development of Therapeutics, Broad Institute, Cambridge, MA, USA
| | - Meghan O'Keefe
- Center for the Development of Therapeutics, Broad Institute, Cambridge, MA, USA
| | | | | | | | | | | | | | | | | | | | | | | | - Adam Skepner
- Center for the Development of Therapeutics, Broad Institute, Cambridge, MA, USA
| | - Donald Raymond
- Center for the Development of Therapeutics, Broad Institute, Cambridge, MA, USA
| | - Salvatore LaRussa
- Center for the Development of Therapeutics, Broad Institute, Cambridge, MA, USA
| | - David C McKinney
- Center for the Development of Therapeutics, Broad Institute, Cambridge, MA, USA
| | | | | | - Dale Porter
- Broad Institute, Cambridge, MA, USA; Cedilla Therapeutics, Cambridge, MA, USA
| | - Andrew J Aguirre
- Broad Institute, Cambridge, MA, USA; Medical Oncology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | | | - Brian McMillan
- Center for the Development of Therapeutics, Broad Institute, Cambridge, MA, USA; Tango Therapeutics, Cambridge, MA, USA
| | - William R Sellers
- Broad Institute, Cambridge, MA, USA; Medical Oncology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, USA.
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13
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Ampudia-Mesias E, Puerta-Martinez F, Bridges M, Zellmer D, Janeiro A, Strokes M, Sham YY, Taher A, Castro MG, Moertel CL, Pluhar GE, Olin MR. CD200 Immune-Checkpoint Peptide Elicits an Anti-glioma Response Through the DAP10 Signaling Pathway. Neurotherapeutics 2021; 18:1980-1994. [PMID: 33829411 PMCID: PMC8609078 DOI: 10.1007/s13311-021-01038-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/11/2021] [Indexed: 02/08/2023] Open
Abstract
Numerous therapies aimed at driving an effective anti-glioma response have been employed over the last decade; nevertheless, survival outcomes for patients remain dismal. This may be due to the expression of immune-checkpoint ligands such as PD-L1 by glioblastoma (GBM) cells which interact with their respective receptors on tumor-infiltrating effector T cells curtailing the activation of anti-GBM CD8+ T cell-mediated responses. Therefore, a combinatorial regimen to abolish immunosuppression would provide a powerful therapeutic approach against GBM. We developed a peptide ligand (CD200AR-L) that binds an uncharacterized CD200 immune-checkpoint activation receptor (CD200AR). We sought to test the hypothesis that CD200AR-L/CD200AR binding signals via he DAP10&12 pathways through in vitro studies by analyzing transcription, protein, and phosphorylation, and in vivo loss of function studies using inhibitors to select signaling molecules. We report that CD200AR-L/CD200AR binding induces an initial activation of the DAP10&12 pathways followed by a decrease in activity within 30 min, followed by reactivation via a positive feedback loop. Further in vivo studies using DAP10&12KO mice revealed that DAP10, but not DAP12, is required for tumor control. When we combined CD200AR-L with an immune-stimulatory gene therapy, in an intracranial GBM model in vivo, we observed increased median survival, and long-term survivors. These studies are the first to characterize the signaling pathway used by the CD200AR, demonstrating a novel strategy for modulating immune checkpoints for immunotherapy currently being analyzed in a phase I adult trial.
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Affiliation(s)
| | - Francisco Puerta-Martinez
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Miurel Bridges
- Bioinformatics and Computational Biology Program, University of Minnesota, Minneapolis, MN, 55455, USA
| | - David Zellmer
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, 55455, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Andrew Janeiro
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Matt Strokes
- Cell Signaling Technology, Inc, Danvers, MA, 09123, USA
| | - Yuk Y Sham
- Bioinformatics and Computational Biology Program, University of Minnesota, Minneapolis, MN, 55455, USA
- Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Ayman Taher
- Department of Neurosurgery and Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Maria G Castro
- Department of Neurosurgery and Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Christopher L Moertel
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, 55455, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55455, USA
| | - G Elizabeth Pluhar
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55455, USA
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Michael R Olin
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, 55455, USA.
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55455, USA.
- University of Minnesota, 2-167 Moos Tower, 515 Delaware St SE, Minneapolis, MN, 55455, USA.
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14
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Stanek TJ, Gennaro VJ, Tracewell MA, Di Marcantonio D, Pauley KL, Butt S, McNair C, Wang F, Kossenkov AV, Knudsen KE, Butt T, Sykes SM, McMahon SB. The SAGA complex regulates early steps in transcription via its deubiquitylase module subunit USP22. EMBO J 2021; 40:e102509. [PMID: 34155658 PMCID: PMC8365265 DOI: 10.15252/embj.2019102509] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 04/10/2021] [Accepted: 04/26/2021] [Indexed: 12/12/2022] Open
Abstract
The SAGA coactivator complex is essential for eukaryotic transcription and comprises four distinct modules, one of which contains the ubiquitin hydrolase USP22. In yeast, the USP22 ortholog deubiquitylates H2B, resulting in Pol II Ser2 phosphorylation and subsequent transcriptional elongation. In contrast to this H2B-associated role in transcription, we report here that human USP22 contributes to the early stages of stimulus-responsive transcription, where USP22 is required for pre-initiation complex (PIC) stability. Specifically, USP22 maintains long-range enhancer-promoter contacts and controls loading of Mediator tail and general transcription factors (GTFs) onto promoters, with Mediator core recruitment being USP22-independent. In addition, we identify Mediator tail subunits MED16 and MED24 and the Pol II subunit RBP1 as potential non-histone substrates of USP22. Overall, these findings define a role for human SAGA within the earliest steps of transcription.
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Affiliation(s)
- Timothy J Stanek
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Victoria J Gennaro
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Mason A Tracewell
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Daniela Di Marcantonio
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Kristen L Pauley
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Sabrina Butt
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Christopher McNair
- Department of Cancer Biology, Sidney Kimmel Medical College and Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | | | | | - Karen E Knudsen
- Department of Cancer Biology, Sidney Kimmel Medical College and Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | | | - Stephen M Sykes
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Steven B McMahon
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
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15
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Global Mass Spectrometry-Based Analysis of Protein Ubiquitination Using K-ε-GG Remnant Antibody Enrichment. Methods Mol Biol 2021; 2365:203-216. [PMID: 34432246 DOI: 10.1007/978-1-0716-1665-9_11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Ubiquitination is a post-translational modification that affects protein degradation as well as a variety of cellular processes. Methods that globally profile ubiquitination are powerful tools to better understand these processes. Here we describe an updated method for identification and quantification of thousands of sites of ubiquitination from cells, tissues, or other biological materials. The method involves cell lysis and digestion to peptides, immunoaffinity enrichment with an antibody recognizing di-glycine remnants left behind at ubiquitinated lysines, and liquid chromatography-tandem mass spectrometry analysis of the enriched peptides.
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16
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Houston R, Sekine S, Calderon MJ, Seifuddin F, Wang G, Kawagishi H, Malide DA, Li Y, Gucek M, Pirooznia M, Nelson AJ, Stokes MP, Stewart-Ornstein J, Mullett SJ, Wendell SG, Watkins SC, Finkel T, Sekine Y. Acetylation-mediated remodeling of the nucleolus regulates cellular acetyl-CoA responses. PLoS Biol 2020; 18:e3000981. [PMID: 33253182 PMCID: PMC7728262 DOI: 10.1371/journal.pbio.3000981] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 12/10/2020] [Accepted: 10/29/2020] [Indexed: 12/14/2022] Open
Abstract
The metabolite acetyl-coenzyme A (acetyl-CoA) serves as an essential element for a wide range of cellular functions including adenosine triphosphate (ATP) production, lipid synthesis, and protein acetylation. Intracellular acetyl-CoA concentrations are associated with nutrient availability, but the mechanisms by which a cell responds to fluctuations in acetyl-CoA levels remain elusive. Here, we generate a cell system to selectively manipulate the nucleo-cytoplasmic levels of acetyl-CoA using clustered regularly interspaced short palindromic repeat (CRISPR)-mediated gene editing and acetate supplementation of the culture media. Using this system and quantitative omics analyses, we demonstrate that acetyl-CoA depletion alters the integrity of the nucleolus, impairing ribosomal RNA synthesis and evoking the ribosomal protein-dependent activation of p53. This nucleolar remodeling appears to be mediated through the class IIa histone deacetylases (HDACs). Our findings highlight acetylation-mediated control of the nucleolus as an important hub linking acetyl-CoA fluctuations to cellular stress responses.
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Affiliation(s)
- Ryan Houston
- Aging Institute, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Shiori Sekine
- Aging Institute, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Division of Cardiology, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Michael J. Calderon
- Department of Cell Biology, Center for Biologic Imaging, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Fayaz Seifuddin
- National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland, United States of America
| | - Guanghui Wang
- National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland, United States of America
| | - Hiroyuki Kawagishi
- National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland, United States of America
| | - Daniela A. Malide
- National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland, United States of America
| | - Yuesheng Li
- National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland, United States of America
| | - Marjan Gucek
- National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland, United States of America
| | - Mehdi Pirooznia
- National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland, United States of America
| | - Alissa J. Nelson
- Cell Signaling Technology, INC., Danvers, Massachusetts, United States of America
| | - Matthew P. Stokes
- Cell Signaling Technology, INC., Danvers, Massachusetts, United States of America
| | - Jacob Stewart-Ornstein
- Department of Computational and Systems Biology, University of Pittsburgh and Hillman Cancer Center, Pittsburgh, Pennsylvania, United States of America
| | - Steven J. Mullett
- Department of Pharmacology and Chemical Biology, the Health Sciences Metabolomics and Lipidomics Core, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Stacy G. Wendell
- Department of Pharmacology and Chemical Biology, the Health Sciences Metabolomics and Lipidomics Core, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Simon C. Watkins
- Department of Cell Biology, Center for Biologic Imaging, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Toren Finkel
- Aging Institute, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Division of Cardiology, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland, United States of America
| | - Yusuke Sekine
- Aging Institute, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland, United States of America
- Division of Endocrinology and Metabolism, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
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17
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Sharma V, Sood R, Khlaifia A, Eslamizade MJ, Hung TY, Lou D, Asgarihafshejani A, Lalzar M, Kiniry SJ, Stokes MP, Cohen N, Nelson AJ, Abell K, Possemato AP, Gal-Ben-Ari S, Truong VT, Wang P, Yiannakas A, Saffarzadeh F, Cuello AC, Nader K, Kaufman RJ, Costa-Mattioli M, Baranov PV, Quintana A, Sanz E, Khoutorsky A, Lacaille JC, Rosenblum K, Sonenberg N. eIF2α controls memory consolidation via excitatory and somatostatin neurons. Nature 2020; 586:412-416. [PMID: 33029011 PMCID: PMC7874887 DOI: 10.1038/s41586-020-2805-8] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 07/06/2020] [Indexed: 12/19/2022]
Abstract
An important tenet of learning and memory is the notion of a molecular switch that promotes the formation of long-term memory1-4. The regulation of proteostasis is a critical and rate-limiting step in the consolidation of new memories5-10. One of the most effective and prevalent ways to enhance memory is by regulating the synthesis of proteins controlled by the translation initiation factor eIF211. Phosphorylation of the α-subunit of eIF2 (p-eIF2α), the central component of the integrated stress response (ISR), impairs long-term memory formation in rodents and birds11-13. By contrast, inhibiting the ISR by mutating the eIF2α phosphorylation site, genetically11 and pharmacologically inhibiting the ISR kinases14-17, or mimicking reduced p-eIF2α with the ISR inhibitor ISRIB11, enhances long-term memory in health and disease18. Here we used molecular genetics to dissect the neuronal circuits by which the ISR gates cognitive processing. We found that learning reduces eIF2α phosphorylation in hippocampal excitatory neurons and a subset of hippocampal inhibitory neurons (those that express somatostatin, but not parvalbumin). Moreover, ablation of p-eIF2α in either excitatory or somatostatin-expressing (but not parvalbumin-expressing) inhibitory neurons increased general mRNA translation, bolstered synaptic plasticity and enhanced long-term memory. Thus, eIF2α-dependent mRNA translation controls memory consolidation via autonomous mechanisms in excitatory and somatostatin-expressing inhibitory neurons.
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Affiliation(s)
- Vijendra Sharma
- Department of Biochemistry, McGill University, Montréal, Québec, Canada.
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montréal, Québec, Canada.
| | - Rapita Sood
- Department of Biochemistry, McGill University, Montréal, Québec, Canada
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montréal, Québec, Canada
| | | | - Mohammad Javad Eslamizade
- Department of Biochemistry, McGill University, Montréal, Québec, Canada
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montréal, Québec, Canada
- Department of Neurosciences, University of Montréal, Montréal, Québec, Canada
| | - Tzu-Yu Hung
- Department of Biochemistry, McGill University, Montréal, Québec, Canada
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montréal, Québec, Canada
| | - Danning Lou
- Department of Biochemistry, McGill University, Montréal, Québec, Canada
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montréal, Québec, Canada
| | | | - Maya Lalzar
- Bioinformatics Services Unit, Faculty of Natural Sciences, University of Haifa, Mount Carmel, Haifa, Israel
| | - Stephen J Kiniry
- School of Biochemistry and Cell Biology, University College Cork, Cork, T12 XF62, Ireland
| | - Matthew P Stokes
- Proteomics Division, Cell Signaling Technology, Danvers, MA, 01923, USA
| | - Noah Cohen
- Department of Biochemistry, McGill University, Montréal, Québec, Canada
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montréal, Québec, Canada
| | - Alissa J Nelson
- Proteomics Division, Cell Signaling Technology, Danvers, MA, 01923, USA
| | - Kathryn Abell
- Proteomics Division, Cell Signaling Technology, Danvers, MA, 01923, USA
| | | | | | - Vinh T Truong
- Department of Biochemistry, McGill University, Montréal, Québec, Canada
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montréal, Québec, Canada
| | - Peng Wang
- Department of Biochemistry, McGill University, Montréal, Québec, Canada
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montréal, Québec, Canada
| | - Adonis Yiannakas
- Sagol Department of Neurobiology, University of Haifa, Haifa, Israel
| | - Fatemeh Saffarzadeh
- Department of Neurosciences, University of Montréal, Montréal, Québec, Canada
| | - A Claudio Cuello
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec, Canada
| | - Karim Nader
- Department of Psychology, McGill University, Montréal, Québec, Canada
| | - Randal J Kaufman
- Degenerative Diseases Program, Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, CA, USA
| | | | - Pavel V Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork, T12 XF62, Ireland
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, RAS, Moscow, Russia
| | - Albert Quintana
- Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, Bellaterra, Spain
- Neuroscience Institute, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Elisenda Sanz
- Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, Bellaterra, Spain
- Neuroscience Institute, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Arkady Khoutorsky
- Department of Anesthesia, McGill University, Montréal, Québec, Canada
- Faculty of Dentistry, McGill University, Montréal, Québec, Canada
| | - Jean-Claude Lacaille
- Department of Neurosciences, University of Montréal, Montréal, Québec, Canada
- Centre for Interdisciplinary Research on Brain and Learning, University of Montréal, Montréal, Québec, Canada
| | - Kobi Rosenblum
- Sagol Department of Neurobiology, University of Haifa, Haifa, Israel.
- Center for Gene Manipulation in the Brain, University of Haifa, Haifa, Israel.
| | - Nahum Sonenberg
- Department of Biochemistry, McGill University, Montréal, Québec, Canada.
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montréal, Québec, Canada.
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18
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Yu X, Liu C, Yang W, Stojkoska A, Cheng G, Yang H, Yue R, Wang J, Liao Y, Sun X, Zhou X, Xie J. Global quantitative phosphoproteome reveals phosphorylation network of bovine lung tissue altered by Mycobacterium bovis. Microb Pathog 2020; 147:104402. [PMID: 32712114 DOI: 10.1016/j.micpath.2020.104402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 06/08/2020] [Accepted: 07/15/2020] [Indexed: 10/23/2022]
Abstract
Bovine tuberculosis caused by Mycobacterium bovis remains a major cause of economic loss in cattle industries worldwide. However, the pathogenic mechanisms remain poorly understood. Post-translation modifications (PTM) such as phosphorylation play a crucial role in pathogenesis. While the change of transcriptome and proteome during the interaction between M. bovis and cattle were studied, there are no reports on the phosphoproteome change. We apply Tandem Mass Tag-based (TMT) quantitative proteomics coupled with immobilized metal-chelated affinity chromatography (IMAC) enrichment to obtain the quantified phosphorylation in vivo of M. bovis infected cattle lung tissue. The phosphorylated proteins are widespread in the nucleus, cytoplasm and plasma membrane. By using a change fold of 1.2, 165 phosphosites from 147 proteins were enriched, with 88 upregulated and 77 downregulated sites respectively. We further constructed the protein-protein interaction (PPI) networks of STAT3, SRRM2 and IRS-1 based on their number of differential phosphorylation sites and KEGG pathways. Similar patterns of gene expression dynamics of selected genes were observed in Mycobacterium tuberculosis infected human sample GEO dataset, implicating crucial roles of these genes in pathogenic Mycobacteria - host interaction. The first phosphorproteome reveals the relationship between bovine tuberculosis and glucose metabolism, and will help further refinement of target proteins for mechanistic study.
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Affiliation(s)
- Xi Yu
- State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Institute of Modern Biopharmaceuticals, Southwest University, Chongqing, 400715, China
| | - Chunfa Liu
- Chinese Center for Disease Control and Prevention, National Tuberculosis Reference Laboratory, Changping, 102206, Beijing, China
| | - Wenmin Yang
- State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Institute of Modern Biopharmaceuticals, Southwest University, Chongqing, 400715, China
| | - Andrea Stojkoska
- State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Institute of Modern Biopharmaceuticals, Southwest University, Chongqing, 400715, China
| | - Guangyu Cheng
- State Key Laboratory of Agrobiotechnology, Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, China Agricultural University, Haidian District, 100193, Beijing, China
| | - Hongjun Yang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Ruichao Yue
- State Key Laboratory of Agrobiotechnology, Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, China Agricultural University, Haidian District, 100193, Beijing, China
| | - Jie Wang
- State Key Laboratory of Agrobiotechnology, Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, China Agricultural University, Haidian District, 100193, Beijing, China
| | - Yi Liao
- State Key Laboratory of Agrobiotechnology, Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, China Agricultural University, Haidian District, 100193, Beijing, China
| | - Xin Sun
- State Key Laboratory of Agrobiotechnology, Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, China Agricultural University, Haidian District, 100193, Beijing, China
| | - Xiangmei Zhou
- State Key Laboratory of Agrobiotechnology, Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, China Agricultural University, Haidian District, 100193, Beijing, China.
| | - Jianping Xie
- State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Institute of Modern Biopharmaceuticals, Southwest University, Chongqing, 400715, China.
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19
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Bonucci M, Kuperwasser N, Barbe S, Koka V, de Villeneuve D, Zhang C, Srivastava N, Jia X, Stokes MP, Bienaimé F, Verkarre V, Lopez JB, Jaulin F, Pontoglio M, Terzi F, Delaval B, Piel M, Pende M. mTOR and S6K1 drive polycystic kidney by the control of Afadin-dependent oriented cell division. Nat Commun 2020; 11:3200. [PMID: 32581239 PMCID: PMC7314806 DOI: 10.1038/s41467-020-16978-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 06/01/2020] [Indexed: 02/08/2023] Open
Abstract
mTOR activation is essential and sufficient to cause polycystic kidneys in Tuberous Sclerosis Complex (TSC) and other genetic disorders. In disease models, a sharp increase of proliferation and cyst formation correlates with a dramatic loss of oriented cell division (OCD). We find that OCD distortion is intrinsically due to S6 kinase 1 (S6K1) activation. The concomitant loss of S6K1 in Tsc1-mutant mice restores OCD but does not decrease hyperproliferation, leading to non-cystic harmonious hyper growth of kidneys. Mass spectrometry-based phosphoproteomics for S6K1 substrates revealed Afadin, a known component of cell-cell junctions required to couple intercellular adhesions and cortical cues to spindle orientation. Afadin is directly phosphorylated by S6K1 and abnormally decorates the apical surface of Tsc1-mutant cells with E-cadherin and α-catenin. Our data reveal that S6K1 hyperactivity alters centrosome positioning in mitotic cells, affecting oriented cell division and promoting kidney cysts in conditions of mTOR hyperactivity.
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Affiliation(s)
- Martina Bonucci
- Institut Necker-Enfants Malades, 14 rue Maria Helena Vieira Da Silva, CS, 61431, Paris, France.,Inserm, U1151, Paris, F-75014, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Nicolas Kuperwasser
- Institut Necker-Enfants Malades, 14 rue Maria Helena Vieira Da Silva, CS, 61431, Paris, France.,Inserm, U1151, Paris, F-75014, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Serena Barbe
- Institut Necker-Enfants Malades, 14 rue Maria Helena Vieira Da Silva, CS, 61431, Paris, France.,Inserm, U1151, Paris, F-75014, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Vonda Koka
- Institut Necker-Enfants Malades, 14 rue Maria Helena Vieira Da Silva, CS, 61431, Paris, France.,Inserm, U1151, Paris, F-75014, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Delphine de Villeneuve
- Institut Necker-Enfants Malades, 14 rue Maria Helena Vieira Da Silva, CS, 61431, Paris, France.,Inserm, U1151, Paris, F-75014, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Chi Zhang
- Institut Necker-Enfants Malades, 14 rue Maria Helena Vieira Da Silva, CS, 61431, Paris, France.,Inserm, U1151, Paris, F-75014, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Nishit Srivastava
- Institut Curie, PSL Research University, CNRS, UMR 144, F-75005, Paris, France
| | - Xiaoying Jia
- Cell Signaling Technology INC, 3 Trask Lane, Danvers, MA, 01923, USA
| | - Matthew P Stokes
- Cell Signaling Technology INC, 3 Trask Lane, Danvers, MA, 01923, USA
| | - Frank Bienaimé
- Institut Necker-Enfants Malades, 14 rue Maria Helena Vieira Da Silva, CS, 61431, Paris, France.,Inserm, U1151, Paris, F-75014, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Virginie Verkarre
- Université de Paris, PARCC, INSERM, Equipe Labellisée par la Ligue contre le Cancer, F-75015, Paris, France.,Assistance Publique-Hôpitaux de Paris (AP-HP centre), Hôpital Européen Georges Pompidou, Département d'anatomo-pathologie, F-75015, Paris, France
| | | | | | - Marco Pontoglio
- Institut Necker-Enfants Malades, 14 rue Maria Helena Vieira Da Silva, CS, 61431, Paris, France.,Inserm, U1151, Paris, F-75014, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Fabiola Terzi
- Institut Necker-Enfants Malades, 14 rue Maria Helena Vieira Da Silva, CS, 61431, Paris, France.,Inserm, U1151, Paris, F-75014, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Benedicte Delaval
- CRBM, CNRS, Univ. Montpellier, Centrosome, cilia and pathologies Lab, 1919 Route de Mende, 34293, Montpellier, France
| | - Matthieu Piel
- Institut Curie, PSL Research University, CNRS, UMR 144, F-75005, Paris, France
| | - Mario Pende
- Institut Necker-Enfants Malades, 14 rue Maria Helena Vieira Da Silva, CS, 61431, Paris, France. .,Inserm, U1151, Paris, F-75014, France. .,Université Paris Descartes, Sorbonne Paris Cité, Paris, France.
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20
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Urick ME, Bell DW. Proteomic profiling of FBXW7-mutant serous endometrial cancer cells reveals upregulation of PADI2, a potential therapeutic target. Cancer Med 2020; 9:3863-3874. [PMID: 32248654 PMCID: PMC7286459 DOI: 10.1002/cam4.3013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 02/29/2020] [Accepted: 03/09/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Despite advancements over the past decade revealing molecular aberrations characteristic of endometrial cancer (EC) subtypes, serous ECs remain difficult to treat and associated with poor outcomes. This is due, in part, to the rarity of these tumors within clinical trials and the inability to directly target the most frequent genomic abnormalities. One of the most commonly somatically mutated genes in serous ECs is the tumor suppressor F-box and WD repeat domain containing 7 (FBXW7). METHODS To identify changes in protein expression associated with FBXW7 mutation, we clustered regularly interspaced short palindromic repeats (CRISPR)-edited ARK4 FBXW7 nonmutant serous EC cells to insert recurrent FBXW7 mutations. We then compared the liquid chromatography tandem mass spectrometry-based proteomic profiles of CRISPR-edited ARK1 and ARK4 serous EC cells to matched parental cells. RESULTS Among distinct total and phosphorylated proteins that were significantly differentially expressed in FBXW7-mutant cell lines compared to matched parental lines, we identified increased PADI2 (peptidyl arginine deiminase 2) expression in all ARK1 and ARK4 CRISPR-edited FBXW7-mutant cell lines. We further confirmed the correlation between FBXW7 mutation and increased PADI2 expression in a third biological background, JHUEM-1 endometrioid EC cells. Finally, we established that PADI2 protein is expressed in primary serous endometrial tumors. CONCLUSION Our findings provide novel insight into proteomic changes associated with FBXW7 mutation in serous ECs and identify PADI2 as a novel potential therapeutic target for these tumors.
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Affiliation(s)
- Mary Ellen Urick
- Cancer Genetics and Comparative Genomics BranchNational Human Genome Research InstituteNational Institutes of HealthBethesdaMDUSA
| | - Daphne W. Bell
- Cancer Genetics and Comparative Genomics BranchNational Human Genome Research InstituteNational Institutes of HealthBethesdaMDUSA
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21
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Hirst NL, Nebel JC, Lawton SP, Walker AJ. Deep phosphoproteome analysis of Schistosoma mansoni leads development of a kinomic array that highlights sex-biased differences in adult worm protein phosphorylation. PLoS Negl Trop Dis 2020; 14:e0008115. [PMID: 32203512 PMCID: PMC7089424 DOI: 10.1371/journal.pntd.0008115] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 02/05/2020] [Indexed: 12/16/2022] Open
Abstract
Although helminth parasites cause enormous suffering worldwide we know little of how protein phosphorylation, one of the most important post-translational modifications used for molecular signalling, regulates their homeostasis and function. This is particularly the case for schistosomes. Herein, we report a deep phosphoproteome exploration of adult Schistosoma mansoni, providing one of the richest phosphoprotein resources for any parasite so far, and employ the data to build the first parasite-specific kinomic array. Complementary phosphopeptide enrichment strategies were used to detect 15,844 unique phosphopeptides mapping to 3,176 proteins. The phosphoproteins were predicted to be involved in a wide range of biological processes and phosphoprotein interactome analysis revealed 55 highly interconnected clusters including those enriched with ribosome, proteasome, phagosome, spliceosome, glycolysis, and signalling proteins. 93 distinct phosphorylation motifs were identified, with 67 providing a ‘footprint’ of protein kinase activity; CaMKII, PKA and CK1/2 were highly represented supporting their central importance to schistosome function. Within the kinome, 808 phosphorylation sites were matched to 136 protein kinases, and 68 sites within 37 activation loops were discovered. Analysis of putative protein kinase-phosphoprotein interactions revealed canonical networks but also novel interactions between signalling partners. Kinomic array analysis of male and female adult worm extracts revealed high phosphorylation of transformation:transcription domain associated protein by both sexes, and CDK and AMPK peptides by females. Moreover, eight peptides including protein phosphatase 2C gamma, Akt, Rho2 GTPase, SmTK4, and the insulin receptor were more highly phosphorylated by female extracts, highlighting their possible importance to female worm function. We envision that these findings, tools and methodology will help drive new research into the functional biology of schistosomes and other helminth parasites, and support efforts to develop new therapeutics for their control. Schistosomes are formidable parasites that cause the debilitating and life-threatening disease human schistosomiasis. We need to better understand the cellular biology of these parasites to develop novel strategies for their control. Within cells, a process called protein phosphorylation controls many aspects of molecular communication or ‘signalling’ and is central to cellular function and homeostasis. Here, using complementary strategies, we have performed the first in-depth characterisation and functional annotation of protein phosphorylation events in schistosomes, providing one of the richest phosphoprotein resources for any parasite to date. Using this knowledge, we have developed a novel tool to simultaneously evaluate signalling processes in these worms and highlight sex-biased differences in adult worm protein phosphorylation. Several proteins were found to be more greatly phosphorylated by female worm extracts, suggesting their possible importance to female worm function. This work will help drive new research into the fundamental biology of schistosomes, as well as related parasites, and will support efforts to develop new drug or vaccine-based therapeutics for their control.
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Affiliation(s)
- Natasha L. Hirst
- School of Life Sciences Pharmacy and Chemistry, Kingston University, Penrhyn Road, Kingston upon Thames, United Kingdom
| | - Jean-Christophe Nebel
- School of Computer Science and Mathematics, Kingston University, Penrhyn Road, Kingston upon Thames, United Kingdom
| | - Scott P. Lawton
- School of Life Sciences Pharmacy and Chemistry, Kingston University, Penrhyn Road, Kingston upon Thames, United Kingdom
| | - Anthony J. Walker
- School of Life Sciences Pharmacy and Chemistry, Kingston University, Penrhyn Road, Kingston upon Thames, United Kingdom
- * E-mail:
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22
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Hamza GM, Bergo VB, Mamaev S, Wojchowski DM, Toran P, Worsfold CR, Castaldi MP, Silva JC. Affinity-Bead Assisted Mass Spectrometry (Affi-BAMS): A Multiplexed Microarray Platform for Targeted Proteomics. Int J Mol Sci 2020; 21:E2016. [PMID: 32188029 PMCID: PMC7139916 DOI: 10.3390/ijms21062016] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 03/10/2020] [Accepted: 03/13/2020] [Indexed: 02/06/2023] Open
Abstract
The ability to quantitatively probe diverse panels of proteins and their post-translational modifications (PTMs) across multiple samples would aid a broad spectrum of biological, biochemical and pharmacological studies. We report a novel, microarray analytical technology that combines immuno-affinity capture with Matrix Assisted Laser Desorption Ionization Mass Spectrometry (MALDI MS), which is capable of supporting highly multiplexed, targeted proteomic assays. Termed "Affinity-Bead Assisted Mass Spectrometry" (Affi-BAMS), this LC-free technology enables development of highly specific and customizable assay panels for simultaneous profiling of multiple proteins and PTMs. While affinity beads have been used previously in combination with MS, the Affi-BAMS workflow uses enrichment on a single bead that contains one type of antibody, generally capturing a single analyte (protein or PTM) while having enough binding capacity to enable quantification within approximately 3 orders of magnitude. The multiplexing capability is achieved by combining Affi-BAMS beads with different protein specificities. To enable screening of bead-captured analytes by MS, we further developed a novel method of performing spatially localized elution of targets from individual beads arrayed on a microscope slide. The resulting arrays of micro spots contain highly concentrated analytes localized within 0.5 mm diameter spots that can be directly measured using MALDI MS. While both intact proteins and protein fragments can be monitored by Affi-BAMS, we initially focused on applying this technology for bottom-up proteomics to enable screening of hundreds of samples per day by combining the robust magnetic bead-based workflow with the high throughput nature of MALDI MS acquisition. To demonstrate the variety of applications and robustness of Affi-BAMS, several studies are presented that focus on the response of 4EBP1, RPS6, ERK1/ERK2, mTOR, Histone H3 and C-MET to stimuli including rapamycin, H2O2, EPO, SU11274, Staurosporine and Vorinostat.
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Affiliation(s)
- Ghaith M. Hamza
- Discovery Sciences, BioPharmaceutical R&D, AstraZeneca, Boston, MA 02451, USA; (G.M.H.); (M.P.C.)
- Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA; (D.M.W.); (P.T.)
| | - Vladislav B. Bergo
- Adeptrix Corporation, Beverly, MA 01915, USA; (V.B.B.); (S.M.); (C.R.W.)
| | - Sergey Mamaev
- Adeptrix Corporation, Beverly, MA 01915, USA; (V.B.B.); (S.M.); (C.R.W.)
| | - Don M. Wojchowski
- Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA; (D.M.W.); (P.T.)
| | - Paul Toran
- Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA; (D.M.W.); (P.T.)
| | | | - M. Paola Castaldi
- Discovery Sciences, BioPharmaceutical R&D, AstraZeneca, Boston, MA 02451, USA; (G.M.H.); (M.P.C.)
| | - Jeffrey C. Silva
- Adeptrix Corporation, Beverly, MA 01915, USA; (V.B.B.); (S.M.); (C.R.W.)
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23
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McCann JJ, Vasilevskaya IA, Poudel Neupane N, Shafi AA, McNair C, Dylgjeri E, Mandigo AC, Schiewer MJ, Schrecengost RS, Gallagher P, Stanek TJ, McMahon SB, Berman-Booty LD, Ostrander WF, Knudsen KE. USP22 Functions as an Oncogenic Driver in Prostate Cancer by Regulating Cell Proliferation and DNA Repair. Cancer Res 2020; 80:430-443. [PMID: 31740444 PMCID: PMC7814394 DOI: 10.1158/0008-5472.can-19-1033] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 10/02/2019] [Accepted: 11/13/2019] [Indexed: 02/06/2023]
Abstract
Emerging evidence indicates the deubiquitinase USP22 regulates transcriptional activation and modification of target substrates to promote pro-oncogenic phenotypes. Here, in vivo characterization of tumor-associated USP22 upregulation and unbiased interrogation of USP22-regulated functions in vitro demonstrated critical roles for USP22 in prostate cancer. Specifically, clinical datasets validated that USP22 expression is elevated in prostate cancer, and a novel murine model demonstrated a hyperproliferative phenotype with prostate-specific USP22 overexpression. Accordingly, upon overexpression or depletion of USP22, enrichment of cell-cycle and DNA repair pathways was observed in the USP22-sensitive transcriptome and ubiquitylome using prostate cancer models of clinical relevance. Depletion of USP22 sensitized cells to genotoxic insult, and the role of USP22 in response to genotoxic insult was further confirmed using mouse adult fibroblasts from the novel murine model of USP22 expression. As it was hypothesized that USP22 deubiquitylates target substrates to promote protumorigenic phenotypes, analysis of the USP22-sensitive ubiquitylome identified the nucleotide excision repair protein, XPC, as a critical mediator of the USP22-mediated response to genotoxic insult. Thus, XPC undergoes deubiquitylation as a result of USP22 function and promotes USP22-mediated survival to DNA damage. Combined, these findings reveal unexpected functions of USP22 as a driver of protumorigenic phenotypes and have significant implications for the role of USP22 in therapeutic outcomes. SIGNIFICANCE: The studies herein present a novel mouse model of tumor-associated USP22 overexpression and implicate USP22 in modulation of cellular survival and DNA repair, in part through regulation of XPC.
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Affiliation(s)
- Jennifer J McCann
- Department of Cancer Biology, Sidney Kimmel Medical College, Philadelphia, Pennsylvania
| | - Irina A Vasilevskaya
- Department of Cancer Biology, Sidney Kimmel Medical College, Philadelphia, Pennsylvania
| | | | - Ayesha A Shafi
- Department of Cancer Biology, Sidney Kimmel Medical College, Philadelphia, Pennsylvania
| | - Christopher McNair
- Department of Cancer Biology, Sidney Kimmel Medical College, Philadelphia, Pennsylvania
| | - Emanuela Dylgjeri
- Department of Cancer Biology, Sidney Kimmel Medical College, Philadelphia, Pennsylvania
| | - Amy C Mandigo
- Department of Cancer Biology, Sidney Kimmel Medical College, Philadelphia, Pennsylvania
| | - Matthew J Schiewer
- Department of Cancer Biology, Sidney Kimmel Medical College, Philadelphia, Pennsylvania
| | - Randy S Schrecengost
- Department of Cancer Biology, Sidney Kimmel Medical College, Philadelphia, Pennsylvania
| | - Peter Gallagher
- Department of Cancer Biology, Sidney Kimmel Medical College, Philadelphia, Pennsylvania
| | - Timothy J Stanek
- Department of Biochemistry & Molecular Biology, Sidney Kimmel Medical College, Philadelphia, Pennsylvania
| | - Steven B McMahon
- Department of Biochemistry & Molecular Biology, Sidney Kimmel Medical College, Philadelphia, Pennsylvania
| | - Lisa D Berman-Booty
- Department of Cancer Biology, Sidney Kimmel Medical College, Philadelphia, Pennsylvania
| | - William F Ostrander
- Department of Cancer Biology, Sidney Kimmel Medical College, Philadelphia, Pennsylvania
| | - Karen E Knudsen
- Department of Cancer Biology, Sidney Kimmel Medical College, Philadelphia, Pennsylvania.
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24
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Synthetic PreImplantation Factor (sPIF) induces posttranslational protein modification and reverses paralysis in EAE mice. Sci Rep 2019; 9:12876. [PMID: 31578341 PMCID: PMC6775138 DOI: 10.1038/s41598-019-48473-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 05/15/2019] [Indexed: 11/24/2022] Open
Abstract
An autoimmune response against myelin protein is considered one of the key pathogenic processes that initiates multiple sclerosis (MS). The currently available MS disease modifying therapies have demonstrated to reduce the frequency of inflammatory attacks. However, they appear limited in preventing disease progression and neurodegeneration. Hence, novel therapeutic approaches targeting both inflammation and neuroregeneration are urgently needed. A new pregnancy derived synthetic peptide, synthetic PreImplantation Factor (sPIF), crosses the blood-brain barrier and prevents neuro-inflammation. We report that sPIF reduces paralysis and de-myelination of the brain in a clinically-relevant experimental autoimmune encephalomyelitis mice model. These effects, at least in part, are due to post-translational modifications, which involve cyclic AMP dependent protein kinase (PKA), calcium-dependent protein kinase (PKC), and immune regulation. In terms of potential MS treatment, sPIF was successfully tested in neurodegenerative animal models of perinatal brain injury and experimental autoimmune encephalitis. Importantly, sPIF received a FDA Fast Track Approval for first in human trial in autommuninty (completed).
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25
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Thompson SM, Jondal DE, Butters KA, Knudsen BE, Anderson JL, Roberts LR, Callstrom MR, Woodrum DA. Heat Stress and Thermal Ablation Induce Local Expression of Nerve Growth Factor Inducible (VGF) in Hepatocytes and Hepatocellular Carcinoma: Preclinical and Clinical Studies. Gene Expr 2018; 19:37-47. [PMID: 29973305 PMCID: PMC6290322 DOI: 10.3727/105221618x15305531034617] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The purposes of this study were to test the hypothesis that heat stress and hepatic thermal ablation induce nerve growth factor inducible (VGF) and to determine intrahepatic versus systemic VGF expression induced by thermal ablation in vivo and in patients. Hepatocytes and HCC cells were subjected to moderate (45°C) or physiologic (37°C) heat stress for 10 min and assessed for VGF expression at 0-72 h post-heat stress (n ≥ 3 experiments). Orthotopic N1S1 HCC-bearing rats were randomized to sham or laser thermal ablation (3 W × 90 s), and liver/serum was harvested at 0-7 days postablation for analysis of VGF expression (n ≥ 6 per group). Serum was collected from patients undergoing thermal ablation for HCC (n = 16) at baseline, 3-6, and 18-24 h postablation and analyzed for VGF expression. Data were analyzed using ordinary or repeated-measures one-way analysis of variance and post hoc pairwise comparison with Dunnett's test. Moderate heat stress induced time-dependent VGF mRNA (3- to 15-fold; p < 0.04) and protein expression and secretion (3.1- to 3.3-fold; p < 0.05). Thermal ablation induced VGF expression at the hepatic ablation margin at 1 and 3 days postablation but not remote from the ablation zone or distant intrahepatic lobe. There was no detectable serum VGF following hepatic thermal ablation in rats and no increase in serum VGF following HCC thermal ablation in patients at 3-6 and 18-24 h postablation compared to baseline (0.71- and 0.63-fold; p = 0.27 and p = 0.16, respectively). Moderate heat stress induces expression and secretion of VGF in HCC cells and hepatocytes in vitro, and thermal ablation induces local intrahepatic but not distant intrahepatic or systemic VGF expression in vivo.
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Affiliation(s)
- Scott M. Thompson
- *Department of Radiology, Mayo Clinic School of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Danielle E. Jondal
- *Department of Radiology, Mayo Clinic School of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Kim A. Butters
- *Department of Radiology, Mayo Clinic School of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Bruce E. Knudsen
- *Department of Radiology, Mayo Clinic School of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Jill L. Anderson
- *Department of Radiology, Mayo Clinic School of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Lewis R. Roberts
- †Division of Gastroenterology and Hepatology, Mayo Clinic School of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Matthew R. Callstrom
- *Department of Radiology, Mayo Clinic School of Medicine, Mayo Clinic, Rochester, MN, USA
| | - David A. Woodrum
- *Department of Radiology, Mayo Clinic School of Medicine, Mayo Clinic, Rochester, MN, USA
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26
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Control of CCND1 ubiquitylation by the catalytic SAGA subunit USP22 is essential for cell cycle progression through G1 in cancer cells. Proc Natl Acad Sci U S A 2018; 115:E9298-E9307. [PMID: 30224477 PMCID: PMC6176615 DOI: 10.1073/pnas.1807704115] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Overexpression of the deubiquitylase ubiquitin-specific peptidase 22 (USP22) is a marker of aggressive cancer phenotypes like metastasis, therapy resistance, and poor survival. Functionally, this overexpression of USP22 actively contributes to tumorigenesis, as USP22 depletion blocks cancer cell cycle progression in vitro, and inhibits tumor progression in animal models of lung, breast, bladder, ovarian, and liver cancer, among others. Current models suggest that USP22 mediates these biological effects via its role in epigenetic regulation as a subunit of the Spt-Ada-Gcn5-acetyltransferase (SAGA) transcriptional cofactor complex. Challenging the dogma, we report here a nontranscriptional role for USP22 via a direct effect on the core cell cycle machinery: that is, the deubiquitylation of the G1 cyclin D1 (CCND1). Deubiquitylation by USP22 protects CCND1 from proteasome-mediated degradation and occurs separately from the canonical phosphorylation/ubiquitylation mechanism previously shown to regulate CCND1 stability. We demonstrate that control of CCND1 is a key mechanism by which USP22 mediates its known role in cell cycle progression. Finally, USP22 and CCND1 levels correlate in patient lung and colorectal cancer samples and our preclinical studies indicate that targeting USP22 in combination with CDK inhibitors may offer an approach for treating cancer patients whose tumors exhibit elevated CCND1.
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27
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Dhillon RS, Richards JG. Hypoxia induces selective modifications to the acetylome in the brain of zebrafish (Danio rerio). Comp Biochem Physiol B Biochem Mol Biol 2018; 224:79-87. [PMID: 29309913 DOI: 10.1016/j.cbpb.2017.12.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 12/18/2017] [Accepted: 12/20/2017] [Indexed: 10/18/2022]
Abstract
Reversible protein acetylation is an important regulatory mechanism for modulating protein function. The cellular protein acetylome is in large part dictated by the cellular redox balance, and in particular [NAD+]. While the relationship between hypoxia, redox balance, energy charge and resulting mitochondrial dysfunction has been examined in the context of hypoxia-linked pathologies, little is known about the direct effects of decreases in environmental oxygen on reversible lysine acetylation, and the resulting modifications to mitochondrial metabolism. To address this knowledge gap, we exposed zebrafish (Danio rerio) to 16 h of hypoxia (2.21 kPa) and quantified acetylation levels of 1220 proteins using whole-cell proteomics in samples of brain taken from normoxic and hypoxic zebrafish. In addition, we examined the effects of hypoxia on cytoplasmic and mitochondrial redox status, whole-cell energetics, the activity of the mitochondrial NAD+-dependent deacetylase SIRT3, and electron transport chain complex activities to determine if there is an association between hypoxia-induced metabolic disturbances, protein acetylation, and mitochondrial function. Our results (1) reveal several key changes in the acetylation status of proteins in the brain, primarily within the mitochondria; (2) show significant fluctuations in cytoplasmic and mitochondrial redox status within the brain during hypoxia exposure; and (3) provide evidence that lysine acetylation may be related to large changes in electron transport and ATP-synthase complex activities and adenylate status in zebrafish exposed to hypoxic stress. Together, these data provide new insights into the role of protein modifications in mitochondrial metabolism during hypoxia.
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Affiliation(s)
- Rashpal S Dhillon
- Wisconsin Institute for Discovery, Department of Biomolecular Chemistry, University of Wisconsin-Madison, 330 North Orchard Street, Madison, WI 53715, USA; Department of Zoology, The University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada.
| | - Jeffrey G Richards
- Department of Zoology, The University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
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28
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Hershberger KA, Abraham DM, Martin AS, Mao L, Liu J, Gu H, Locasale JW, Hirschey MD. Sirtuin 5 is required for mouse survival in response to cardiac pressure overload. J Biol Chem 2017; 292:19767-19781. [PMID: 28972174 PMCID: PMC5712617 DOI: 10.1074/jbc.m117.809897] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 09/16/2017] [Indexed: 01/05/2023] Open
Abstract
In mitochondria, the sirtuin SIRT5 is an NAD+-dependent protein deacylase that controls several metabolic pathways. Although a wide range of SIRT5 targets have been identified, the overall function of SIRT5 in organismal metabolic homeostasis remains unclear. Given that SIRT5 expression is highest in the heart and that sirtuins are commonly stress-response proteins, we used an established model of pressure overload-induced heart muscle hypertrophy caused by transverse aortic constriction (TAC) to determine SIRT5's role in cardiac stress responses. Remarkably, SIRT5KO mice had reduced survival upon TAC compared with wild-type mice but exhibited no mortality when undergoing a sham control operation. The increased mortality with TAC was associated with increased pathological hypertrophy and with key abnormalities in both cardiac performance and ventricular compliance. By combining high-resolution MS-based metabolomic and proteomic analyses of cardiac tissues from wild-type and SIRT5KO mice, we found several biochemical abnormalities exacerbated in the SIRT5KO mice, including apparent decreases in fatty acid oxidation and glucose oxidation as well as an overall decrease in mitochondrial NAD+/NADH. Together, these abnormalities suggest that SIRT5 deacylates protein substrates involved in cellular oxidative metabolism to maintain mitochondrial energy production. Overall, the functional and metabolic results presented here suggest an accelerated development of cardiac dysfunction in SIRT5KO mice in response to TAC, explaining increased mortality upon cardiac stress. Our findings reveal a key role for SIRT5 in maintaining cardiac oxidative metabolism under pressure overload to ensure survival.
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Affiliation(s)
- Kathleen A Hershberger
- From the Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, North Carolina 27701
- the Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710
| | - Dennis M Abraham
- the Department of Medicine, Division of Cardiology and Duke Cardiovascular Physiology Core, Duke University Medical Center, Durham, North Carolina 27710
| | - Angelical S Martin
- From the Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, North Carolina 27701
- the Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710
| | - Lan Mao
- the Department of Medicine, Division of Cardiology and Duke Cardiovascular Physiology Core, Duke University Medical Center, Durham, North Carolina 27710
| | - Juan Liu
- From the Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, North Carolina 27701
- the Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710
| | - Hongbo Gu
- Cell Signaling Technology Inc., Danvers, Massachusetts 01923, and
| | - Jason W Locasale
- From the Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, North Carolina 27701
- the Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710
| | - Matthew D Hirschey
- From the Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, North Carolina 27701,
- the Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710
- the Division of Endocrinology, Metabolism, and Nutrition, Department of Medicine, Duke University Medical Center, Durham, North Carolina 27710
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Thompson SM, Jondal DE, Butters KA, Knudsen BE, Anderson JL, Stokes MP, Jia X, Grande JP, Roberts LR, Callstrom MR, Woodrum DA. Heat stress induced, ligand-independent MET and EGFR signalling in hepatocellular carcinoma. Int J Hyperthermia 2017; 34:812-823. [PMID: 28954551 DOI: 10.1080/02656736.2017.1385859] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
PURPOSE The aims of the present study were 2-fold: first, to test the hypothesis that heat stress induces MET and EGFR signalling in hepatocellular carcinoma (HCC) cells and inhibition of this signalling decreases HCC clonogenic survival; and second, to identify signalling pathways associated with heat stress induced MET signalling. MATERIALS AND METHODS MET+ and EGFR+ HCC cells were pre-treated with inhibitors to MET, EGFR, PI3K/mTOR or vehicle and subjected to heat stress or control ± HGF or EGF growth factors and assessed by colony formation assay, Western blotting and/or quantitative mass spectrometry. IACUC approved partial laser thermal or sham ablation was performed on orthotopic N1S1 and AS30D HCC tumours and liver/tumour assessed for phospho-MET and phospho-EGFR immunostaining. RESULTS Heat-stress induced rapid MET and EGFR phosphorylation that is distinct from HGF or EGF in HCC cells and thermal ablation induced MET but not EGFR phosphorylation at the HCC tumour ablation margin. Inhibition of the MET and EGFR blocked both heat stress and growth factor induced MET and EGFR phosphorylation and inhibition of MET decreased HCC clonogenic survival following heat stress. Pathway analysis of quantitative phosphoproteomic data identified downstream pathways associated with heat stress induced MET signalling including AKT, ERK, Stat3 and JNK. However, inhibition of heat stress induced MET signalling did not block AKT signalling. CONCLUSIONS Heat-stress induced MET and EGFR signalling is distinct from growth factor mediated signalling in HCC cells and MET inhibition enhances heat stress induced HCC cell killing via a PI3K/AKT/mTOR-independent mechanism.
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Affiliation(s)
- Scott M Thompson
- a Department of Radiology , Mayo Clinic School of Medicine , Rochester , MN , USA
| | - Danielle E Jondal
- a Department of Radiology , Mayo Clinic School of Medicine , Rochester , MN , USA
| | - Kim A Butters
- a Department of Radiology , Mayo Clinic School of Medicine , Rochester , MN , USA
| | - Bruce E Knudsen
- a Department of Radiology , Mayo Clinic School of Medicine , Rochester , MN , USA
| | - Jill L Anderson
- a Department of Radiology , Mayo Clinic School of Medicine , Rochester , MN , USA
| | - Matthew P Stokes
- b Cell Signaling Technology, Inc. 3 Trask Ln. Danvers , MA , USA
| | - Xiaoying Jia
- b Cell Signaling Technology, Inc. 3 Trask Ln. Danvers , MA , USA
| | - Joseph P Grande
- c Department of Laboratory Medicine and Pathology , Mayo Clinic School of Medicine , Rochester , MN , USA
| | - Lewis R Roberts
- d Division of Gastroenterology and Hepatology , Mayo Clinic School of Medicine , Rochester , MN , USA
| | - Matthew R Callstrom
- a Department of Radiology , Mayo Clinic School of Medicine , Rochester , MN , USA
| | - David A Woodrum
- a Department of Radiology , Mayo Clinic School of Medicine , Rochester , MN , USA
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30
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Targeting neuronal activity-regulated neuroligin-3 dependency in high-grade glioma. Nature 2017; 549:533-537. [PMID: 28959975 PMCID: PMC5891832 DOI: 10.1038/nature24014] [Citation(s) in RCA: 311] [Impact Index Per Article: 44.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 08/22/2017] [Indexed: 12/14/2022]
Abstract
High-grade gliomas (HGG) are a devastating group of cancers, representing the leading cause of brain tumor-related death in both children and adults. Therapies aimed at mechanisms intrinsic to the glioma cell have translated to only limited success; effective therapeutic strategies will need to also target elements of the tumor microenvironment that promote glioma progression. We recently demonstrated that neuronal activity robustly promotes the growth of a range of molecularly and clinically distinct HGG types, including adult glioblastoma (GBM), anaplastic oligodendroglioma, pediatric GBM, and diffuse intrinsic pontine glioma (DIPG)1. An important mechanism mediating this neural regulation of brain cancer is activity-dependent cleavage and secretion of the synaptic molecule neuroligin-3 (NLGN3), which promotes glioma proliferation through the PI3K-mTOR pathway1. However, neuroligin-3 necessity to glioma growth, proteolytic mechanism of secretion and further molecular consequences in glioma remain to be clarified. Here, we demonstrate a striking dependence of HGG growth on microenvironmental neuroligin-3, elucidate signaling cascades downstream of neuroligin-3 binding in glioma and determine a therapeutically targetable mechanism of secretion. Patient-derived orthotopic xenografts of pediatric GBM, DIPG and adult GBM fail to grow in Nlgn3 knockout mice. Neuroligin-3 stimulates numerous oncogenic pathways, including early focal adhesion kinase activation upstream of PI3K-mTOR, and induces transcriptional changes including upregulation of numerous synapse-related genes in glioma cells. Neuroligin-3 is cleaved from both neurons and oligodendrocyte precursor cells via the ADAM10 sheddase. ADAM10 inhibitors prevent release of neuroligin-3 into the tumor microenvironment and robustly block HGG xenograft growth. This work defines a promising strategy for targeting neuroligin-3 secretion, which could prove transformative for HGG therapy.
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Bian Y, Li L, Dong M, Liu X, Kaneko T, Cheng K, Liu H, Voss C, Cao X, Wang Y, Litchfield D, Ye M, Li SSC, Zou H. Ultra-deep tyrosine phosphoproteomics enabled by a phosphotyrosine superbinder. Nat Chem Biol 2016; 12:959-966. [DOI: 10.1038/nchembio.2178] [Citation(s) in RCA: 111] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 07/11/2016] [Indexed: 12/26/2022]
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Standish AJ, Teh MY, Tran ENH, Doyle MT, Baker PJ, Morona R. Unprecedented Abundance of Protein Tyrosine Phosphorylation Modulates Shigella flexneri Virulence. J Mol Biol 2016; 428:4197-4208. [PMID: 27380737 DOI: 10.1016/j.jmb.2016.06.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 06/06/2016] [Accepted: 06/23/2016] [Indexed: 01/09/2023]
Abstract
Evidence is accumulating that protein tyrosine phosphorylation plays a crucial role in the ability of important human bacterial pathogens to cause disease. While most works have concentrated on its role in the regulation of a major bacterial virulence factor, the polysaccharide capsule, recent studies have suggested a much broader role for this post-translational modification. This prompted us to investigate protein tyrosine phosphorylation in the human pathogen Shigella flexneri. We first completed a tyrosine phosphoproteome, identifying 905 unique tyrosine phosphorylation sites on at least 573 proteins (approximately 15% of all proteins). This is the most tyrosine-phosphorylated sites and proteins in a single bacterium identified to date, substantially more than the level seen in eukaryotic cells. Most had not previously been identified and included proteins encoded by the virulence plasmid, which is essential for S. flexneri to invade cells and cause disease. In order to investigate the function of these phosphorylation sites in important virulence factors, phosphomimetic and ablative mutations were constructed in the type 3 secretion system ATPase Spa47 and the master virulence regulator VirB. This revealed that tyrosine residues phosphorylated in our study are critical for Spa47 and VirB activity, and tyrosine phosphorylation likely regulates their functional activity and subsequently the virulence of this major human pathogen. This study suggests that tyrosine phosphorylation plays a critical role in regulating a wide variety of virulence factors in the human pathogen S. flexneri and serves as a base for future studies defining its complete role.
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Affiliation(s)
- Alistair James Standish
- Research Centre for Infectious Diseases, Department of Molecular and Cellular Biology, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia.
| | - Min Yan Teh
- Research Centre for Infectious Diseases, Department of Molecular and Cellular Biology, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Elizabeth Ngoc Hoa Tran
- Research Centre for Infectious Diseases, Department of Molecular and Cellular Biology, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Matthew Thomas Doyle
- Research Centre for Infectious Diseases, Department of Molecular and Cellular Biology, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Paul J Baker
- Research Centre for Infectious Diseases, Department of Molecular and Cellular Biology, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Renato Morona
- Research Centre for Infectious Diseases, Department of Molecular and Cellular Biology, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
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