1
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Tal MC, Hansen PS, Ogasawara HA, Feng Q, Volk RF, Lee B, Casebeer SE, Blacker GS, Shoham M, Galloway SD, Sapiro AL, Hayes B, Torrez Dulgeroff LB, Raveh T, Pothineni VR, Potula HHSK, Rajadas J, Bastounis EE, Chou S, Robinson WH, Coburn J, Weissman IL, Zaro BW. P66 is a bacterial mimic of CD47 that binds the anti-phagocytic receptor SIRPα and facilitates macrophage evasion by Borrelia burgdorferi. bioRxiv 2024:2024.04.29.591704. [PMID: 38746193 PMCID: PMC11092639 DOI: 10.1101/2024.04.29.591704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Innate immunity, the first line of defense against pathogens, relies on efficient elimination of invading agents by phagocytes. In the co-evolution of host and pathogen, pathogens developed mechanisms to dampen and evade phagocytic clearance. Here, we report that bacterial pathogens can evade clearance by macrophages through mimicry at the mammalian anti-phagocytic "don't eat me" signaling axis between CD47 (ligand) and SIRPα (receptor). We identified a protein, P66, on the surface of Borrelia burgdorferi that, like CD47, is necessary and sufficient to bind the macrophage receptor SIRPα. Expression of the gene encoding the protein is required for bacteria to bind SIRPα or a high-affinity CD47 reagent. Genetic deletion of p66 increases phagocytosis by macrophages. Blockade of P66 during infection promotes clearance of the bacteria. This study demonstrates that mimicry of the mammalian anti-phagocytic protein CD47 by B. burgdorferi inhibits macrophage-mediated bacterial clearance. Such a mechanism has broad implications for understanding of host-pathogen interactions and expands the function of the established innate immune checkpoint receptor SIRPα. Moreover, this report reveals P66 as a novel therapeutic target in the treatment of Lyme Disease.
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Affiliation(s)
- Michal Caspi Tal
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Ludwig Center for Cancer Stem Cell Research and Medicine, and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Paige S. Hansen
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Ludwig Center for Cancer Stem Cell Research and Medicine, and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Haley A. Ogasawara
- Department of Pharmaceutical Chemistry, The Cardiovascular Research Institute, Helen Diller Family Comprehensive Cancer Center, Quantitative Biosciences Institute, School of Pharmacy, University of California, San Francisco, CA, USA
| | - Qingying Feng
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Regan F. Volk
- Department of Pharmaceutical Chemistry, The Cardiovascular Research Institute, Helen Diller Family Comprehensive Cancer Center, Quantitative Biosciences Institute, School of Pharmacy, University of California, San Francisco, CA, USA
| | - Brandon Lee
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sara E. Casebeer
- Department of Pharmaceutical Chemistry, The Cardiovascular Research Institute, Helen Diller Family Comprehensive Cancer Center, Quantitative Biosciences Institute, School of Pharmacy, University of California, San Francisco, CA, USA
| | - Grace S. Blacker
- Institute for Stem Cell Biology and Regenerative Medicine, Ludwig Center for Cancer Stem Cell Research and Medicine, and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Sarah D. Galloway
- Institute for Stem Cell Biology and Regenerative Medicine, Ludwig Center for Cancer Stem Cell Research and Medicine, and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Anne L. Sapiro
- Department of Biochemistry and Biophysics, School of Medicine, University of California, San Francisco, CA, USA
| | | | - Laughing Bear Torrez Dulgeroff
- Institute for Stem Cell Biology and Regenerative Medicine, Ludwig Center for Cancer Stem Cell Research and Medicine, and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Tal Raveh
- Institute for Stem Cell Biology and Regenerative Medicine, Ludwig Center for Cancer Stem Cell Research and Medicine, and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Venkata Raveendra Pothineni
- Advanced Drug Delivery and Regenerative Biomaterials Laboratory, Dept of Medicine, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Hari-Hara SK Potula
- Institute for Stem Cell Biology and Regenerative Medicine, Ludwig Center for Cancer Stem Cell Research and Medicine, and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
- Advanced Drug Delivery and Regenerative Biomaterials Laboratory, Dept of Medicine, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Jayakumar Rajadas
- Advanced Drug Delivery and Regenerative Biomaterials Laboratory, Dept of Medicine, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Effie E. Bastounis
- Interfaculty Institute of Microbiology and Infection Medicine, Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Seemay Chou
- Department of Biochemistry and Biophysics, School of Medicine, University of California, San Francisco, CA, USA
| | - William H. Robinson
- Division of Immunology and Rheumatology, Departement of Medicine, Stanford Unversity School of Medicine, Stanford, CA, USA
| | - Jenifer Coburn
- Departments of Medicine and Microbiology and Immunology, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, USA
| | - Irving L. Weissman
- Institute for Stem Cell Biology and Regenerative Medicine, Ludwig Center for Cancer Stem Cell Research and Medicine, and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Balyn W. Zaro
- Department of Pharmaceutical Chemistry, The Cardiovascular Research Institute, Helen Diller Family Comprehensive Cancer Center, Quantitative Biosciences Institute, School of Pharmacy, University of California, San Francisco, CA, USA
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2
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Chuh KN, Zaro BW, Piller F, Piller V, Pratt MR. Correction to "Changes in Metabolic Chemical Reporter Structure Yield a Selective Probe of O-GlcNAc Modification". J Am Chem Soc 2023; 145:22284. [PMID: 37774147 PMCID: PMC10571073 DOI: 10.1021/jacs.3c08368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Indexed: 10/01/2023]
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3
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Sapiro AL, Hayes BM, Volk RF, Zhang JY, Brooks DM, Martyn C, Radkov A, Zhao Z, Kinnersley M, Secor PR, Zaro BW, Chou S. Longitudinal map of transcriptome changes in the Lyme pathogen Borrelia burgdorferi during tick-borne transmission. eLife 2023; 12:RP86636. [PMID: 37449477 PMCID: PMC10393048 DOI: 10.7554/elife.86636] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023] Open
Abstract
Borrelia burgdorferi (Bb), the causative agent of Lyme disease, adapts to vastly different environments as it cycles between tick vector and vertebrate host. During a tick bloodmeal, Bb alters its gene expression to prepare for vertebrate infection; however, the full range of transcriptional changes that occur over several days inside of the tick are technically challenging to capture. We developed an experimental approach to enrich Bb cells to longitudinally define their global transcriptomic landscape inside nymphal Ixodes scapularis ticks during a transmitting bloodmeal. We identified 192 Bb genes that substantially change expression over the course of the bloodmeal from 1 to 4 days after host attachment. The majority of upregulated genes encode proteins found at the cell envelope or proteins of unknown function, including 45 outer surface lipoproteins embedded in the unusual protein-rich coat of Bb. As these proteins may facilitate Bb interactions with the host, we utilized mass spectrometry to identify candidate tick proteins that physically associate with Bb. The Bb enrichment methodology along with the ex vivo Bb transcriptomes and candidate tick interacting proteins presented here provide a resource to facilitate investigations into key determinants of Bb priming and transmission during the tick stage of its unique transmission cycle.
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Affiliation(s)
- Anne L Sapiro
- Department of Biochemistry & Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Beth M Hayes
- Department of Biochemistry & Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Regan F Volk
- Department of Pharmaceutical Chemistry and Cardiovascular Research Institute, University of California, San FranciscoSan FranciscoUnited States
| | - Jenny Y Zhang
- Department of Biochemistry & Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Diane M Brooks
- Division of Biological Sciences, University of MontanaMissoulaUnited States
| | - Calla Martyn
- Department of Biochemistry & Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Atanas Radkov
- Department of Biochemistry & Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Ziyi Zhao
- Department of Biochemistry & Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Margie Kinnersley
- Division of Biological Sciences, University of MontanaMissoulaUnited States
| | - Patrick R Secor
- Division of Biological Sciences, University of MontanaMissoulaUnited States
| | - Balyn W Zaro
- Department of Pharmaceutical Chemistry and Cardiovascular Research Institute, University of California, San FranciscoSan FranciscoUnited States
| | - Seemay Chou
- Department of Biochemistry & Biophysics, University of California, San FranciscoSan FranciscoUnited States
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4
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Chen Z, Mondal A, Abderemane-Ali F, Jang S, Niranjan S, Montaño JL, Zaro BW, Minor DL. EMC chaperone-Ca V structure reveals an ion channel assembly intermediate. Nature 2023; 619:410-419. [PMID: 37196677 PMCID: PMC10896479 DOI: 10.1038/s41586-023-06175-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 05/05/2023] [Indexed: 05/19/2023]
Abstract
Voltage-gated ion channels (VGICs) comprise multiple structural units, the assembly of which is required for function1,2. Structural understanding of how VGIC subunits assemble and whether chaperone proteins are required is lacking. High-voltage-activated calcium channels (CaVs)3,4 are paradigmatic multisubunit VGICs whose function and trafficking are powerfully shaped by interactions between pore-forming CaV1 or CaV2 CaVα1 (ref. 3), and the auxiliary CaVβ5 and CaVα2δ subunits6,7. Here we present cryo-electron microscopy structures of human brain and cardiac CaV1.2 bound with CaVβ3 to a chaperone-the endoplasmic reticulum membrane protein complex (EMC)8,9-and of the assembled CaV1.2-CaVβ3-CaVα2δ-1 channel. These structures provide a view of an EMC-client complex and define EMC sites-the transmembrane (TM) and cytoplasmic (Cyto) docks; interaction between these sites and the client channel causes partial extraction of a pore subunit and splays open the CaVα2δ-interaction site. The structures identify the CaVα2δ-binding site for gabapentinoid anti-pain and anti-anxiety drugs6, show that EMC and CaVα2δ interactions with the channel are mutually exclusive, and indicate that EMC-to-CaVα2δ hand-off involves a divalent ion-dependent step and CaV1.2 element ordering. Disruption of the EMC-CaV complex compromises CaV function, suggesting that the EMC functions as a channel holdase that facilitates channel assembly. Together, the structures reveal a CaV assembly intermediate and EMC client-binding sites that could have wide-ranging implications for the biogenesis of VGICs and other membrane proteins.
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Affiliation(s)
- Zhou Chen
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | - Abhisek Mondal
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | - Fayal Abderemane-Ali
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA
- Department of Physiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Seil Jang
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | - Sangeeta Niranjan
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | - José L Montaño
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
| | - Balyn W Zaro
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
| | - Daniel L Minor
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA.
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA.
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, CA, USA.
- Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, CA, USA.
- Molecular Biophysics and Integrated Bio-imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.
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5
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Datta R, Gholampour MA, Yang CD, Volk R, Lin S, Podolsky MJ, Arnold T, Rieder F, Zaro BW, Verzi M, Lehner R, Abumrad N, Lizama CO, Atabai K. MFGE8 links absorption of dietary fatty acids with catabolism of enterocyte lipid stores through HNF4γ-dependent transcription of CES enzymes. Cell Rep 2023; 42:112249. [PMID: 36924494 PMCID: PMC10138282 DOI: 10.1016/j.celrep.2023.112249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 12/21/2022] [Accepted: 02/25/2023] [Indexed: 03/17/2023] Open
Abstract
Enterocytes modulate the extent of postprandial lipemia by storing dietary fats in cytoplasmic lipid droplets (cLDs). We have previously shown that the integrin ligand MFGE8 links absorption of dietary fats with activation of triglyceride (TG) hydrolases that catabolize cLDs for chylomicron production. Here, we identify CES1D as the key hydrolase downstream of the MFGE8-αvβ5 integrin pathway that regulates catabolism of diet-derived cLDs. Mfge8 knockout (KO) enterocytes have reduced CES1D transcript and protein levels and reduced protein levels of the transcription factor HNF4γ. Both Ces1d and Hnf4γ KO mice have decreased enterocyte TG hydrolase activity coupled with retention of TG in cLDs. Mechanistically, MFGE8-dependent fatty acid uptake through CD36 stabilizes HNF4γ protein level; HNF4γ then increases Ces1d transcription. Our work identifies a regulatory network that regulates the severity of postprandial lipemia by linking dietary fat absorption with protein stabilization of a transcription factor that increases expression of hydrolases responsible for catabolizing diet-derived cLDs.
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Affiliation(s)
- Ritwik Datta
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Mohammad A Gholampour
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Christopher D Yang
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Regan Volk
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Sinan Lin
- Department of Gastroenterology, Hepatology and Nutrition, Digestive Diseases and Surgery Institute, Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44106, USA
| | - Michael J Podolsky
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Thomas Arnold
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Florian Rieder
- Department of Gastroenterology, Hepatology and Nutrition, Digestive Diseases and Surgery Institute, Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44106, USA
| | - Balyn W Zaro
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | | | - Richard Lehner
- Department of Pediatrics, University of Alberta, Edmonton, AB T6G 1C9, Canada
| | - Nada Abumrad
- Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Carlos O Lizama
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kamran Atabai
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Lung Biology Center, University of California, San Francisco, San Francisco, CA 94143, USA.
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6
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Dang EV, Lei S, Radkov A, Volk RF, Zaro BW, Madhani HD. Secreted fungal virulence effector triggers allergic inflammation via TLR4. Nature 2022; 608:161-167. [PMID: 35896747 PMCID: PMC9744105 DOI: 10.1038/s41586-022-05005-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 06/21/2022] [Indexed: 12/14/2022]
Abstract
Invasive fungal pathogens are major causes of human mortality and morbidity1,2. Although numerous secreted effector proteins that reprogram innate immunity to promote virulence have been identified in pathogenic bacteria, so far, there are no examples of analogous secreted effector proteins produced by human fungal pathogens. Cryptococcus neoformans, the most common cause of fungal meningitis and a major pathogen in AIDS, induces a pathogenic type 2 response characterized by pulmonary eosinophilia and alternatively activated macrophages3-8. Here, we identify CPL1 as an effector protein secreted by C. neoformans that drives alternative activation (also known as M2 polarization) of macrophages to enable pulmonary infection in mice. We observed that CPL1-enhanced macrophage polarization requires Toll-like receptor 4, which is best known as a receptor for bacterial endotoxin but is also a poorly understood mediator of allergen-induced type 2 responses9-12. We show that this effect is caused by CPL1 itself and not by contaminating lipopolysaccharide. CPL1 is essential for virulence, drives polarization of interstitial macrophages in vivo, and requires type 2 cytokine signalling for its effect on infectivity. Notably, C. neoformans associates selectively with polarized interstitial macrophages during infection, suggesting a mechanism by which C. neoformans generates its own intracellular replication niche within the host. This work identifies a circuit whereby a secreted effector protein produced by a human fungal pathogen reprograms innate immunity, revealing an unexpected role for Toll-like receptor 4 in promoting the pathogenesis of infectious disease.
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Affiliation(s)
- Eric V. Dang
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, United States of America
| | - Susan Lei
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, United States of America
| | - Atanas Radkov
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, United States of America
| | - Regan F. Volk
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, United States of America,Cardiovascular Research Institute, University of California, San Francisco, CA, United States of America
| | - Balyn W. Zaro
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, United States of America,Cardiovascular Research Institute, University of California, San Francisco, CA, United States of America
| | - Hiten D. Madhani
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, United States of America,Chan-Zuckerberg Biohub, San Francisco, CA, United States of America,
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7
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Volk RF, Montaño JL, Warrington SE, Hofmann KL, Zaro BW. Proteomic characterization of phagocytic primary human monocyte-derived macrophages. RSC Chem Biol 2022; 3:783-793. [PMID: 35755185 PMCID: PMC9175098 DOI: 10.1039/d2cb00076h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 05/12/2022] [Indexed: 11/21/2022] Open
Abstract
Macrophages play a vital role in the innate immune system, identifying and destroying unwanted cells. However, it has been difficult to attain a comprehensive understanding of macrophage protein abundance due to technical limitations. In addition, it remains unclear how changes in proteome composition are linked to phagocytic activity. In this study we developed methods to derive human macrophages and prepare them for mass spectrometry analysis in order to more-deeply understand the proteomic consequences of macrophage stimulation. Interferon gamma (IF-g), an immune stimulating cytokine, was used to induce macrophage activation, increasing phagocytosis of cancer cells by 2-fold. These conditions were used to perform comparative shotgun proteomics between resting macrophages and stimulated macrophages with increased phagocytic activity. Our analysis revealed that macrophages bias their protein production toward biological processes associated with phagocytosis and antigen processing in response to stimulation. We confirmed our findings by antibody-based western blotting experiments, validating both previously reported and novel proteins of interest. In addition to whole protein changes, we evaluated active protein synthesis by treating cells with the methionine surrogate probe homopropargylglycine (HPG). We saw increased rates of HPG incorporation during phagocytosis-inducing stimulation, suggesting protein synthesis rates are altered by stimulation. Together our findings provide the most comprehensive proteomic insight to date into primary human macrophages. We anticipate that this data can be used as a launchpoint to generate new hypotheses about innate immune function.
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Affiliation(s)
- Regan F Volk
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, Quantitative Biosciences Institute, and Helen Diller Family Comprehensive Cancer Centre, University of California San Francisco CA USA
| | - José L Montaño
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, Quantitative Biosciences Institute, and Helen Diller Family Comprehensive Cancer Centre, University of California San Francisco CA USA
| | - Sara E Warrington
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, Quantitative Biosciences Institute, and Helen Diller Family Comprehensive Cancer Centre, University of California San Francisco CA USA
| | - Katherine L Hofmann
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, Quantitative Biosciences Institute, and Helen Diller Family Comprehensive Cancer Centre, University of California San Francisco CA USA
| | - Balyn W Zaro
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, Quantitative Biosciences Institute, and Helen Diller Family Comprehensive Cancer Centre, University of California San Francisco CA USA
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8
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Montaño JL, Wang BJ, Volk RF, Warrington SE, Garda VG, Hofmann KL, Chen LC, Zaro BW. Improved Electrophile Design for Exquisite Covalent Molecule Selectivity. ACS Chem Biol 2022; 17:1440-1449. [PMID: 35587148 DOI: 10.1021/acschembio.1c00980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Covalent inhibitors are viable therapeutics. However, off-target reactivity challenges the field. Chemists have attempted to solve this issue by varying the reactivity attributes of electrophilic warheads. Here, we report the development of an approach to increase the selectivity of covalent molecules that is independent of warhead reactivity features and can be used in concert with existing methods. Using the scaffold of the Bruton's tyrosine kinase (BTK) inhibitor Ibrutinib for our proof-of-concept, we reasoned that increasing the steric bulk of fumarate-based electrophiles on Ibrutinib should improve selectivity via the steric exclusion of off-targets but retain rates of cysteine reactivity comparable to that of an acrylamide. Using chemical proteomic techniques, we demonstrate that elaboration of the electrophile to a tert-butyl (t-Bu) fumarate ester decreases time-dependent off-target reactivity and abolishes time-independent off-target reactivity. While an alkyne-bearing probe analogue of Ibrutinib has 247 protein targets, our t-Bu fumarate probe analogue has only 7. Of these 7 targets, BTK is the only time-independent target. The t-Bu inhibitor itself is also more selective for BTK, reducing off-targets by 70%. We investigated the consequences of treatment with Ibrutinib and our t-Bu analogue and discovered that only 8 proteins are downregulated in response to treatment with the t-Bu analogue compared to 107 with Ibrutinib. Of these 8 proteins, 7 are also downregulated by Ibrutinib and a majority of these targets are associated with BTK biology. Taken together, these findings reveal an opportunity to increase cysteine-reactive covalent inhibitor selectivity through electrophilic structure optimization.
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Affiliation(s)
- José L. Montaño
- Department of Pharmaceutical Chemistry and Cardiovascular Research Institute, University of California, San Francisco, California 94158, United States
| | - Brian J. Wang
- Department of Pharmaceutical Chemistry and Cardiovascular Research Institute, University of California, San Francisco, California 94158, United States
| | - Regan F. Volk
- Department of Pharmaceutical Chemistry and Cardiovascular Research Institute, University of California, San Francisco, California 94158, United States
| | - Sara E. Warrington
- Department of Pharmaceutical Chemistry and Cardiovascular Research Institute, University of California, San Francisco, California 94158, United States
| | - Virginia G. Garda
- Department of Pharmaceutical Chemistry and Cardiovascular Research Institute, University of California, San Francisco, California 94158, United States
| | - Katherine L. Hofmann
- Department of Pharmaceutical Chemistry and Cardiovascular Research Institute, University of California, San Francisco, California 94158, United States
| | - Leo C. Chen
- Department of Pharmaceutical Chemistry and Cardiovascular Research Institute, University of California, San Francisco, California 94158, United States
| | - Balyn W. Zaro
- Department of Pharmaceutical Chemistry and Cardiovascular Research Institute, University of California, San Francisco, California 94158, United States
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9
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Bouffard E, Zaro BW, Dix MM, Cravatt B, Wong CH. Refinement of Covalent EGFR Inhibitor AZD9291 to Eliminate Off-target Activity. Tetrahedron Lett 2021; 74:153178. [PMID: 34764521 PMCID: PMC8577418 DOI: 10.1016/j.tetlet.2021.153178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Non-small-cell lung cancer (NSCLC) is a major disease that accounts for 85% of all lung cancer cases which claimed around 1.8 billion lives worldwide in 2020. Tyrosine kinase inhibitors (TKIs) that target EGFR have been used for the treatment of NSCLC, but often develop drug resistance, and the covalent inhibitor AZD9291 has been developed to tackle the problem of drug resistance mediated by the T790M EGFR mutation; however, there is a side effect of hyperglycemia that may be due to off-target activity. This study examines analogues of AZD9291 by chemical proteomics, identifying analogues that maintain T790M-EGFR engagement while showing reduced cross-reactivity with off-targets.
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Affiliation(s)
- Elise Bouffard
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
| | - Balyn W Zaro
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
| | - Melissa M Dix
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
| | - Benjamin Cravatt
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
| | - Chi-Huey Wong
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
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10
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Pedowitz NJ, Zaro BW, Pratt MR. Metabolic Labeling for the Visualization and Identification of Potentially O-GlcNAc-Modified Proteins. ACTA ACUST UNITED AC 2021; 12:e81. [PMID: 32289208 DOI: 10.1002/cpch.81] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
O-GlcNAcylation is a posttranslational modification involving the addition of the single monosaccharide N-acetylglucosamine (GlcNAc) onto serine and threonine residues of intracellular proteins. Though O-GlcNAc is found on ∼1000 proteins in mammals, its specific function on individual substrates remains largely a mystery. To overcome this shortcoming, work has been put toward developing metabolic chemical reporters (MCRs) to label O-GlcNAcylated proteins for subsequent biochemical analysis. Typically, these MCRs are GlcNAc or GalNAc analogs functionalized with azide or alkyne handles. These unnatural sugar moieties can be metabolically incorporated directly on to protein substrates. The protocols outlined in this article describe how to use MCRs as tools for visualizing and identifying potentially O-GlcNAc modified proteins via in-gel fluorescence, Western blotting, and mass spectrometry. Taken together, MCR labeling provides a powerful tool to discover where and when substrates are O-GlcNAc modified. © 2020 by John Wiley & Sons, Inc. Basic Protocol 1: Treatment of cells and CuAAC Basic Protocol 2: In-gel fluorescence of labeled cell lysates (1 mg scale) Basic Protocol 3: Enrichment of labeled proteins, trypsinolysis, and collection of peptides for proteomics Basic Protocol 4: Proteomic identification of labeled proteins.
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Affiliation(s)
- Nichole J Pedowitz
- Department of Chemistry, University of Southern California, Los Angeles, California
| | - Balyn W Zaro
- Department of Pharmaceutical Chemistry and The Cardiovascular Research Institute, University of California San Francisco, San Francisco, California
| | - Matthew R Pratt
- Department of Chemistry, University of Southern California, Los Angeles, California.,Department of Biological Sciences, University of Southern California, Los Angeles, California
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11
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Zaro BW, Noh JJ, Mascetti VL, Demeter J, George B, Zukowska M, Gulati GS, Sinha R, Flynn RA, Banuelos A, Zhang A, Wilkinson AC, Jackson P, Weissman IL. Proteomic analysis of young and old mouse hematopoietic stem cells and their progenitors reveals post-transcriptional regulation in stem cells. eLife 2020; 9:e62210. [PMID: 33236985 PMCID: PMC7688314 DOI: 10.7554/elife.62210] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 11/16/2020] [Indexed: 12/13/2022] Open
Abstract
The balance of hematopoietic stem cell (HSC) self-renewal and differentiation is critical for a healthy blood supply; imbalances underlie hematological diseases. The importance of HSCs and their progenitors have led to their extensive characterization at genomic and transcriptomic levels. However, the proteomics of hematopoiesis remains incompletely understood. Here we report a proteomics resource from mass spectrometry of mouse young adult and old adult mouse HSCs, multipotent progenitors and oligopotent progenitors; 12 cell types in total. We validated differential protein levels, including confirmation that Dnmt3a protein levels are undetected in young adult mouse HSCs until forced into cycle. Additionally, through integrating proteomics and RNA-sequencing datasets, we identified a subset of genes with apparent post-transcriptional repression in young adult mouse HSCs. In summary, we report proteomic coverage of young and old mouse HSCs and progenitors, with broader implications for understanding mechanisms for stem cell maintenance, niche interactions and fate determination.
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Affiliation(s)
- Balyn W Zaro
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of MedicineStanfordUnited States
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of MedicineStanfordUnited States
| | - Joseph J Noh
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of MedicineStanfordUnited States
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of MedicineStanfordUnited States
| | - Victoria L Mascetti
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of MedicineStanfordUnited States
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of MedicineStanfordUnited States
| | - Janos Demeter
- Baxter Laboratory, Department of Microbiology and Immunology and Department of Pathology, Stanford University School of MedicineStanfordUnited States
| | - Benson George
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of MedicineStanfordUnited States
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of MedicineStanfordUnited States
| | - Monika Zukowska
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of MedicineStanfordUnited States
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of MedicineStanfordUnited States
| | - Gunsagar S Gulati
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of MedicineStanfordUnited States
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of MedicineStanfordUnited States
| | - Rahul Sinha
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of MedicineStanfordUnited States
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of MedicineStanfordUnited States
| | - Ryan A Flynn
- Department of Chemistry, Stanford UniversityStanfordUnited States
| | - Allison Banuelos
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of MedicineStanfordUnited States
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of MedicineStanfordUnited States
| | - Allison Zhang
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of MedicineStanfordUnited States
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of MedicineStanfordUnited States
| | - Adam C Wilkinson
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of MedicineStanfordUnited States
| | - Peter Jackson
- Baxter Laboratory, Department of Microbiology and Immunology and Department of Pathology, Stanford University School of MedicineStanfordUnited States
| | - Irving L Weissman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of MedicineStanfordUnited States
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of MedicineStanfordUnited States
- Department of Developmental Biology and the Stanford UC-Berkeley Stem Cell InstituteStanfordUnited States
- Department of Pathology, Stanford University School of MedicineStanfordUnited States
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12
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Darabedian N, Yang B, Ding R, Cutolo G, Zaro BW, Woo CM, Pratt MR. O-Acetylated Chemical Reporters of Glycosylation Can Display Metabolism-Dependent Background Labeling of Proteins but Are Generally Reliable Tools for the Identification of Glycoproteins. Front Chem 2020; 8:318. [PMID: 32411667 PMCID: PMC7198827 DOI: 10.3389/fchem.2020.00318] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 03/30/2020] [Indexed: 12/13/2022] Open
Abstract
Monosaccharide analogs bearing bioorthogonal functionalities, or metabolic chemical reporters (MCRs) of glycosylation, have been used for approximately two decades for the visualization and identification of different glycoproteins. More recently, proteomics analyses have shown that per-O-acetylated MCRs can directly and chemically react with cysteine residues in lysates and potentially cells, drawing into question the physiological relevance of the labeling. Here, we report robust metabolism-dependent labeling by Ac42AzMan but not the structurally similar Ac44AzGal. However, the levels of background chemical-labeling of cell lysates by both reporters are low and identical. We then characterized Ac42AzMan labeling and found that the vast majority of the labeling occurs on intracellular proteins but that this MCR is not converted to previously characterized reporters of intracellular O-GlcNAc modification. Additionally, we used isotope targeted glycoproteomics (IsoTaG) proteomics to show that essentially all of the Ac42AzMan labeling is on cysteine residues. Given the implications this result has for the identification of intracellular O-GlcNAc modifications using MCRs, we then performed a meta-analysis of the potential O-GlcNAcylated proteins identified by different techniques. We found that many of the proteins identified by MCRs have also been found by other methods. Finally, we randomly selected four proteins that had only been identified as O-GlcNAcylated by MCRs and showed that half of them were indeed modified. Together, these data indicate that the selective metabolism of certain MCRs is responsible for S-glycosylation of proteins in the cytosol and nucleus. However, these results also show that MCRs are still good tools for unbiased identification of glycosylated proteins, as long as complementary methods are employed for confirmation.
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Affiliation(s)
- Narek Darabedian
- Department of Chemistry, University of Southern California, Los Angeles, CA, United States
| | - Bo Yang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, United States
| | - Richie Ding
- Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - Giuliano Cutolo
- Department of Chemistry, University of Southern California, Los Angeles, CA, United States
| | - Balyn W Zaro
- Department of Biological Science, University of Southern California, San Francisco, CA, United States
| | - Christina M Woo
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, United States
| | - Matthew R Pratt
- Department of Chemistry, University of Southern California, Los Angeles, CA, United States.,Biological Sciences, University of Southern California, Los Angeles, CA, United States
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13
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Barkal AA, Brewer RE, Markovic M, Kowarsky M, Barkal SA, Zaro BW, Krishnan V, Hatakeyama J, Dorigo O, Barkal LJ, Weissman IL. CD24 signalling through macrophage Siglec-10 is a target for cancer immunotherapy. Nature 2019; 572:392-396. [PMID: 31367043 PMCID: PMC6697206 DOI: 10.1038/s41586-019-1456-0] [Citation(s) in RCA: 668] [Impact Index Per Article: 133.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 07/02/2019] [Indexed: 02/06/2023]
Abstract
Ovarian cancer and triple-negative breast cancer (TNBC) are among the most lethal diseases affecting women, with few targeted therapies and high rates of metastasis. Here we show that CD24 can be the dominant innate immune checkpoint in ovarian cancer and breast cancer, and is a new, promising target for cancer immunotherapy. Cancer cells are capable of evading clearance by macrophages through the overexpression of anti-phagocytic surface proteins, called “don’t eat me” signals, including CD471, programmed cell death ligand 1 (PD-L1)2, and the beta-2 microglobulin subunit of the major histocompatibility class I complex (B2M)3. Monoclonal antibodies which antagonize the interaction of “don’t eat me” signals with their macrophage-expressed receptors have demonstrated therapeutic potential in several cancers4–5. However, variability in the magnitude and durability of the response to these agents has suggested the presence of additional, as yet unknown, “don’t eat me” signals. Here we demonstrate a novel role for tumor-expressed CD24 in promoting immune evasion through its interaction with the inhibitory receptor, Sialic Acid Binding Ig Like Lectin 10 (Siglec-10), expressed by tumor-associated macrophages (TAMs). We observe that many tumors overexpress CD24 and that TAMs express high levels of Siglec-10. Both genetic ablation of CD24 or Siglec-10, and monoclonal antibody blockade of the CD24–Siglec-10 interaction, robustly augment the phagocytosis of all CD24-expressing human tumors tested. Genetic ablation as well as therapeutic blockade of CD24 resulted in a macrophage-dependent reduction of tumor growth and extension of survival, in vivo. These data highlight CD24 as a highly-expressed, anti-phagocytic signal in several cancers and demonstrate the therapeutic potential for CD24-blockade as cancer immunotherapy.
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Affiliation(s)
- Amira A Barkal
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA.,Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA.,Stanford Medical Scientist Training Program, Stanford University, Stanford, CA, USA
| | - Rachel E Brewer
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA.,Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Maxim Markovic
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA.,Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Mark Kowarsky
- Department of Physics, Stanford University, Stanford, CA, USA
| | - Sammy A Barkal
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Balyn W Zaro
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA.,Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Venkatesh Krishnan
- Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jason Hatakeyama
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA.,Department of Urology, Stanford University School of Medicine, Stanford, CA, USA
| | - Oliver Dorigo
- Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, Stanford University School of Medicine, Stanford, CA, USA
| | - Layla J Barkal
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Irving L Weissman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA. .,Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of Medicine, Stanford, CA, USA. .,Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA. .,Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
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14
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Senkane K, Vinogradova EV, Suciu RM, Crowley VM, Zaro BW, Bradshaw JM, Brameld KA, Cravatt BF. The Proteome‐Wide Potential for Reversible Covalency at Cysteine. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201905829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Kristine Senkane
- Department of ChemistryThe Scripps Research Institute La Jolla CA 92037 USA
| | | | - Radu M. Suciu
- Department of ChemistryThe Scripps Research Institute La Jolla CA 92037 USA
| | - Vincent M. Crowley
- Department of ChemistryThe Scripps Research Institute La Jolla CA 92037 USA
| | - Balyn W. Zaro
- Department of ChemistryThe Scripps Research Institute La Jolla CA 92037 USA
| | | | - Ken A. Brameld
- Principia Biopharma 220 E. Grand Avenue South San Francisco CA 94080 USA
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15
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Senkane K, Vinogradova EV, Suciu RM, Crowley VM, Zaro BW, Bradshaw JM, Brameld KA, Cravatt BF. The Proteome-Wide Potential for Reversible Covalency at Cysteine. Angew Chem Int Ed Engl 2019; 58:11385-11389. [PMID: 31222866 DOI: 10.1002/anie.201905829] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Indexed: 01/06/2023]
Abstract
Reversible covalency, achieved with, for instance, highly electron-deficient olefins, offers a compelling strategy to design chemical probes and drugs that benefit from the sustained target engagement afforded by irreversible compounds, while avoiding permanent protein modification. Reversible covalency has mainly been evaluated for cysteine residues in individual kinases and the broader potential for this strategy to engage cysteines across the proteome remains unexplored. Herein, we describe a mass-spectrometry-based platform that integrates gel filtration with activity-based protein profiling to assess cysteine residues across the human proteome for both irreversible and reversible interactions with small-molecule electrophiles. Using this method, we identify numerous cysteine residues from diverse protein classes that are reversibly engaged by cyanoacrylamide fragment electrophiles, revealing the broad potential for reversible covalency as a strategy for chemical-probe discovery.
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Affiliation(s)
- Kristine Senkane
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | | | - Radu M Suciu
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Vincent M Crowley
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Balyn W Zaro
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - J Michael Bradshaw
- Principia Biopharma, 220 E. Grand Avenue, South San Francisco, CA, 94080, USA
| | - Ken A Brameld
- Principia Biopharma, 220 E. Grand Avenue, South San Francisco, CA, 94080, USA
| | - Benjamin F Cravatt
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, 92037, USA
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16
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Zaro BW, Vinogradova EV, Lazar DC, Blewett MM, Suciu RM, Takaya J, Studer S, de la Torre JC, Casanova JL, Cravatt BF, Teijaro JR. Dimethyl Fumarate Disrupts Human Innate Immune Signaling by Targeting the IRAK4-MyD88 Complex. J Immunol 2019; 202:2737-2746. [PMID: 30885957 DOI: 10.4049/jimmunol.1801627] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 02/26/2019] [Indexed: 12/14/2022]
Abstract
Dimethyl fumarate (DMF) is a prescribed treatment for multiple sclerosis and has also been used to treat psoriasis. The electrophilicity of DMF suggests that its immunosuppressive activity is related to the covalent modification of cysteine residues in the human proteome. Nonetheless, our understanding of the proteins modified by DMF in human immune cells and the functional consequences of these reactions remains incomplete. In this study, we report that DMF inhibits human plasmacytoid dendritic cell function through a mechanism of action that is independent of the major electrophile sensor NRF2. Using chemical proteomics, we instead identify cysteine 13 of the innate immune kinase IRAK4 as a principal cellular target of DMF. We show that DMF blocks IRAK4-MyD88 interactions and IRAK4-mediated cytokine production in a cysteine 13-dependent manner. Our studies thus identify a proteomic hotspot for DMF action that constitutes a druggable protein-protein interface crucial for initiating innate immune responses.
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Affiliation(s)
- Balyn W Zaro
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037
| | | | - Daniel C Lazar
- Department of Immunology and Infectious Disease, The Scripps Research Institute, La Jolla, CA 92037; and
| | - Megan M Blewett
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037
| | - Radu M Suciu
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037
| | - Junichiro Takaya
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037
| | - Sean Studer
- Department of Immunology and Infectious Disease, The Scripps Research Institute, La Jolla, CA 92037; and
| | - Juan Carlos de la Torre
- Department of Immunology and Infectious Disease, The Scripps Research Institute, La Jolla, CA 92037; and
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065
| | - Benjamin F Cravatt
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037;
| | - John R Teijaro
- Department of Immunology and Infectious Disease, The Scripps Research Institute, La Jolla, CA 92037; and
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17
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Walter LA, Batt AR, Darabedian N, Zaro BW, Pratt MR. Azide- and Alkyne-Bearing Metabolic Chemical Reporters of Glycosylation Show Structure-Dependent Feedback Inhibition of the Hexosamine Biosynthetic Pathway. Chembiochem 2018; 19:1918-1921. [PMID: 29979493 PMCID: PMC6261355 DOI: 10.1002/cbic.201800280] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Indexed: 12/18/2022]
Abstract
Metabolic chemical reporters (MCRs) of protein glycosylation are analogues of natural monosaccharides that bear reactive groups, like azides and alkynes. When they are added to living cells and organisms, these small molecules are biosynthetically transformed into nucleotide donor sugars and then used by glycosyltransferases to modify proteins. Subsequent installation of tags by bioorthogonal chemistries can then enable the visualization and enrichment of these glycoproteins. Although this two-step procedure is powerful, the use of MCRs has the potential to change the endogenous production of the natural repertoire of donor sugars. A major route for the generation of these glycosyltransferase substrates is the hexosamine biosynthetic pathway (HBP), which results in uridine diphosphate N-acetylglucosamine (UDP-GlcNAc). Interestingly, the rate-determining enzyme of the HBP, glutamine fructose-6-phosphate amidotransferase (GFAT), is feedback inhibited by UDP-GlcNAc. This raises the possibility that a build-up of UDP-MCRs would block the biosynthesis of UDP-GlcNAc, resulting in off target effects. Here, we directly test this possibility with recombinant human GFAT and a small panel of synthetic UDP-MCRs. We find that MCRs with larger substitutions at the N-acetyl position do not inhibit GFAT, whereas those with modifications of the 2- or 6-hydroxy group do. These results further illuminate the considerations that should be applied to the use of MCRs.
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Affiliation(s)
- Lisa A. Walter
- Department of Chemistry, University of Southern California 840 Downey Way, LJS 250, Los Angeles, CA, 90089 (USA)
| | - Anna R. Batt
- Department of Chemistry, University of Southern California 840 Downey Way, LJS 250, Los Angeles, CA, 90089 (USA)
| | - Narek Darabedian
- Department of Chemistry, University of Southern California 840 Downey Way, LJS 250, Los Angeles, CA, 90089 (USA)
| | - Balyn W. Zaro
- Department of Chemistry, University of Southern California 840 Downey Way, LJS 250, Los Angeles, CA, 90089 (USA)
| | - Matthew R. Pratt
- Department of Chemistry, University of Southern California 840 Downey Way, LJS 250, Los Angeles, CA, 90089 (USA)
- Department of Biological Sciences, University of Southern California 840 Downey Way, LJS 250, Los Angeles, CA, 90089 (USA)
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18
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Bateman LA, Zaro BW, Miller SM, Pratt MR. Correction to "An Alkyne-Aspirin Chemical Reporter for the Detection of Aspirin-Dependent Protein Modification in Living Cells". J Am Chem Soc 2018; 140:4954. [PMID: 29589917 DOI: 10.1021/jacs.8b03225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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19
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Batt AR, Zaro BW, Navarro MX, Pratt MR. Metabolic Chemical Reporters of Glycans Exhibit Cell-Type-Selective Metabolism and Glycoprotein Labeling. Chembiochem 2017; 18:1177-1182. [PMID: 28231413 PMCID: PMC5580397 DOI: 10.1002/cbic.201700020] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Indexed: 12/21/2022]
Abstract
Since the pioneering work by Reutter and co-workers that demonstrated structural flexibility in the carbohydrate biosynthesis and glycosylation pathways, many different labs have used unnatural monosaccharide analogues to perform glycan engineering on the surface of living cells. A subset of these unnatural monosaccharides contain bioorthogonal groups that enable the selective installation of visualization or enrichment tags. These metabolic chemical reporters (MCRs) have proven to be powerful for the unbiased identification of glycoproteins; however, they do have certain limitations. For example, they are incorporated substoichiometrically into glycans, and most MCRs are not selective for one class (e.g., O-GlcNAcylation) of glycoprotein. Here, we explore the relationship between the biosynthesis of MCR donor sugars in cells and the labeling levels of four different N-acetylglucosamine- and N-acetylgalactosamine-based MCRs. We found that the buildup of the different donor sugars correlated well with the overall labeling levels but less so with intracellular labeling of proteins by O-GlcNAcylation.
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Affiliation(s)
- Anna R. Batt
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089
| | - Balyn W. Zaro
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089
| | - Marisol X. Navarro
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089
| | - Matthew R. Pratt
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089
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20
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Chuh KN, Batt AR, Zaro BW, Darabedian N, Marotta NP, Brennan CK, Amirhekmat A, Pratt MR. The New Chemical Reporter 6-Alkynyl-6-deoxy-GlcNAc Reveals O-GlcNAc Modification of the Apoptotic Caspases That Can Block the Cleavage/Activation of Caspase-8. J Am Chem Soc 2017; 139:7872-7885. [PMID: 28528544 PMCID: PMC6225779 DOI: 10.1021/jacs.7b02213] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
O-GlcNAc modification (O-GlcNAcylation) is required for survival in mammalian cells. Genetic and biochemical experiments have found that increased modification inhibits apoptosis in tissues and cell culture and that lowering O-GlcNAcylation induces cell death. However, the molecular mechanisms by which O-GlcNAcylation might inhibit apoptosis are still being elucidated. Here, we first synthesize a new metabolic chemical reporter, 6-Alkynyl-6-deoxy-GlcNAc (6AlkGlcNAc), for the identification of O-GlcNAc-modified proteins. Subsequent characterization of 6AlkGlcNAc shows that this probe is selectively incorporated into O-GlcNAcylated proteins over cell-surface glycoproteins. Using this probe, we discover that the apoptotic caspases are O-GlcNAcylated, which we confirmed using other techniques, raising the possibility that the modification affects their biochemistry. We then demonstrate that changes in the global levels of O-GlcNAcylation result in a converse change in the kinetics of caspase-8 activation during apoptosis. Finally, we show that caspase-8 is modified at residues that can block its cleavage/activation. Our results provide the first evidence that the caspases may be directly affected by O-GlcNAcylation as a potential antiapoptotic mechanism.
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Affiliation(s)
- Kelly N. Chuh
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0744, United States
| | - Anna R. Batt
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0744, United States
| | - Balyn W. Zaro
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0744, United States
| | - Narek Darabedian
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0744, United States
| | - Nicholas P. Marotta
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0744, United States
| | - Caroline K. Brennan
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0744, United States
| | - Arya Amirhekmat
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0744, United States
| | - Matthew R. Pratt
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0744, United States
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089-0744, United States
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21
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Zaro BW, Batt AR, Chuh KN, Navarro MX, Pratt MR. The Small Molecule 2-Azido-2-deoxy-glucose Is a Metabolic Chemical Reporter of O-GlcNAc Modifications in Mammalian Cells, Revealing an Unexpected Promiscuity of O-GlcNAc Transferase. ACS Chem Biol 2017; 12:787-794. [PMID: 28135057 DOI: 10.1021/acschembio.6b00877] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Glycans can be directly labeled using unnatural monosaccharide analogs, termed metabolic chemical reporters (MCRs). These compounds enable the secondary visualization and identification of glycoproteins by taking advantage of bioorthogonal reactions. Most widely used MCRs have azides or alkynes at the 2-N-acetyl position but are not selective for one class of glycoprotein over others. To address this limitation, we are exploring additional MCRs that have bioorthogonal functionality at other positions. Here, we report the characterization of 2-azido-2-deoxy-glucose (2AzGlc). We find that 2AzGlc selectively labels intracellular O-GlcNAc modifications, which further supports a somewhat unexpected, structural flexibility in this pathway. In contrast to the endogenous modification N-acetyl-glucosamine (GlcNAc), we find that 2AzGlc is not dynamically removed from protein substrates and that treatment with higher concentrations of per-acetylated 2AzGlc is toxic to cells. Finally, we demonstrate that this toxicity is an inherent property of the small-molecule, as removal of the 6-acetyl-group renders the corresponding reporter nontoxic but still results in protein labeling.
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Affiliation(s)
- Balyn W. Zaro
- Department
of Chemistry and ‡Department of Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089-0744, United States
| | - Anna R. Batt
- Department
of Chemistry and ‡Department of Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089-0744, United States
| | - Kelly N. Chuh
- Department
of Chemistry and ‡Department of Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089-0744, United States
| | - Marisol X. Navarro
- Department
of Chemistry and ‡Department of Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089-0744, United States
| | - Matthew R. Pratt
- Department
of Chemistry and ‡Department of Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089-0744, United States
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22
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Zaro BW, Whitby LR, Lum KM, Cravatt BF. Metabolically Labile Fumarate Esters Impart Kinetic Selectivity to Irreversible Inhibitors. J Am Chem Soc 2016; 138:15841-15844. [PMID: 27960302 DOI: 10.1021/jacs.6b10589] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Electrophilic small molecules are an important class of chemical probes and drugs that produce biological effects by irreversibly modifying proteins. Examples of electrophilic drugs include covalent kinase inhibitors that are used to treat cancer and the multiple sclerosis drug dimethyl fumarate. Optimized covalent drugs typically inactivate their protein targets rapidly in cells, but ensuing time-dependent, off-target protein modification can erode selectivity and diminish the utility of reactive small molecules as chemical probes and therapeutics. Here, we describe an approach to confer kinetic selectivity to electrophilic drugs. We show that an analogue of the covalent Bruton's tyrosine kinase (BTK) inhibitor Ibrutinib bearing a fumarate ester electrophile is vulnerable to enzymatic metabolism on a time-scale that preserves rapid and sustained BTK inhibition, while thwarting more slowly accumulating off-target reactivity in cell and animal models. These findings demonstrate that metabolically labile electrophilic groups can endow covalent drugs with kinetic selectivity to enable perturbation of proteins and biochemical pathways with greater precision.
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Affiliation(s)
- Balyn W Zaro
- The Skaggs Institute for Chemical Biology and Department of Chemical Physiology , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Landon R Whitby
- The Skaggs Institute for Chemical Biology and Department of Chemical Physiology , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Kenneth M Lum
- The Skaggs Institute for Chemical Biology and Department of Chemical Physiology , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Benjamin F Cravatt
- The Skaggs Institute for Chemical Biology and Department of Chemical Physiology , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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23
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Blewett MM, Xie J, Zaro BW, Backus KM, Altman A, Teijaro JR, Cravatt BF. Chemical proteomic map of dimethyl fumarate-sensitive cysteines in primary human T cells. Sci Signal 2016; 9:rs10. [PMID: 27625306 DOI: 10.1126/scisignal.aaf7694] [Citation(s) in RCA: 128] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Dimethyl fumarate (DMF) is an electrophilic drug that is used to treat autoimmune conditions, including multiple sclerosis and psoriasis. The mechanism of action of DMF is unclear but may involve the covalent modification of proteins or DMF serving as a prodrug that is converted to monomethyl fumarate (MMF). We found that DMF, but not MMF, blocked the activation of primary human and mouse T cells. Using a quantitative, site-specific chemical proteomic platform, we determined the DMF sensitivity of >2400 cysteine residues in human T cells. Cysteines sensitive to DMF, but not MMF, were identified in several proteins with established biochemical or genetic links to T cell function, including protein kinase Cθ (PKCθ). DMF blocked the association of PKCθ with the costimulatory receptor CD28 by perturbing a CXXC motif in the C2 domain of this kinase. Mutation of these DMF-sensitive cysteines also impaired PKCθ-CD28 interactions and T cell activation, designating the C2 domain of PKCθ as a key functional, electrophile-sensing module important for T cell biology.
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Affiliation(s)
- Megan M Blewett
- Department of Chemical Physiology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Jiji Xie
- Division of Cell Biology, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Balyn W Zaro
- Department of Chemical Physiology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Keriann M Backus
- Department of Chemical Physiology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Amnon Altman
- Division of Cell Biology, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - John R Teijaro
- Department of Chemical Physiology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA. Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Benjamin F Cravatt
- Department of Chemical Physiology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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24
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Chesarino NM, Hach JC, Chen JL, Zaro BW, Rajaram MV, Turner J, Schlesinger LS, Pratt MR, Hang HC, Yount JS. Chemoproteomics reveals Toll-like receptor fatty acylation. BMC Biol 2014; 12:91. [PMID: 25371237 PMCID: PMC4240870 DOI: 10.1186/s12915-014-0091-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 10/20/2014] [Indexed: 01/01/2023] Open
Abstract
Background Palmitoylation is a 16-carbon lipid post-translational modification that increases protein hydrophobicity. This form of protein fatty acylation is emerging as a critical regulatory modification for multiple aspects of cellular interactions and signaling. Despite recent advances in the development of chemical tools for the rapid identification and visualization of palmitoylated proteins, the palmitoyl proteome has not been fully defined. Here we sought to identify and compare the palmitoylated proteins in murine fibroblasts and dendritic cells. Results A total of 563 putative palmitoylation substrates were identified, more than 200 of which have not been previously suggested to be palmitoylated in past proteomic studies. Here we validate the palmitoylation of several new proteins including Toll-like receptors (TLRs) 2, 5 and 10, CD80, CD86, and NEDD4. Palmitoylation of TLR2, which was uniquely identified in dendritic cells, was mapped to a transmembrane domain-proximal cysteine. Inhibition of TLR2 S-palmitoylation pharmacologically or by cysteine mutagenesis led to decreased cell surface expression and a decreased inflammatory response to microbial ligands. Conclusions This work identifies many fatty acylated proteins involved in fundamental cellular processes as well as cell type-specific functions, highlighting the value of examining the palmitoyl proteomes of multiple cell types. S-palmitoylation of TLR2 is a previously unknown immunoregulatory mechanism that represents an entirely novel avenue for modulation of TLR2 inflammatory activity. Electronic supplementary material The online version of this article (doi:10.1186/s12915-014-0091-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nicholas M Chesarino
- Department of Microbial Infection and Immunity, Center for Microbial Interface Biology, The Ohio State University, Columbus, OH, 43210, USA.
| | - Jocelyn C Hach
- Department of Microbial Infection and Immunity, Center for Microbial Interface Biology, The Ohio State University, Columbus, OH, 43210, USA.
| | - James L Chen
- Biomedical Informatics, Internal Medicine in the Division of Medical Oncology, The Ohio State University, Columbus, OH, 43210, USA.
| | - Balyn W Zaro
- Departments of Chemistry and Molecular and Computational Biology, University of Southern California, Los Angeles, CA, 90089, USA.
| | - Murugesan Vs Rajaram
- Department of Microbial Infection and Immunity, Center for Microbial Interface Biology, The Ohio State University, Columbus, OH, 43210, USA.
| | - Joanne Turner
- Department of Microbial Infection and Immunity, Center for Microbial Interface Biology, The Ohio State University, Columbus, OH, 43210, USA.
| | - Larry S Schlesinger
- Department of Microbial Infection and Immunity, Center for Microbial Interface Biology, The Ohio State University, Columbus, OH, 43210, USA.
| | - Matthew R Pratt
- Departments of Chemistry and Molecular and Computational Biology, University of Southern California, Los Angeles, CA, 90089, USA.
| | - Howard C Hang
- Laboratory of Chemical Biology and Microbial Pathogenesis, Rockefeller University, New York, NY, 10065, USA.
| | - Jacob S Yount
- Department of Microbial Infection and Immunity, Center for Microbial Interface Biology, The Ohio State University, Columbus, OH, 43210, USA.
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Abstract
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Metabolic
chemical reporters have been largely used to study posttranslational
modifications. Generally, it was assumed that these reporters entered
one biosynthetic pathway, resulting in labeling of one type of modification.
However, because they are metabolized by cells before their addition
onto proteins, metabolic chemical reporters potentially provide a
unique opportunity to read-out on both modifications of interest and
cellular metabolism. We report here the development of a metabolic
chemical reporter 1-deoxy-N-pentynyl glucosamine
(1-deoxy-GlcNAlk). This small-molecule cannot be incorporated into
glycans; however, treatment of mammalian cells results in labeling
of a variety proteins and enables their visualization and identification.
Competition of this labeling with sodium acetate and an acetyltransferase
inhibitor suggests that 1-deoxy-GlcNAlk can enter the protein acetylation
pathway. These results demonstrate that metabolic chemical reporters
have the potential to isolate and potentially discover cross-talk
between metabolic pathways in living cells.
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Affiliation(s)
- Balyn W. Zaro
- Department of Chemistry and ‡Department of
Molecular and Computational
Biology, University of Southern California, Los Angeles, California 90089, United States
| | - Kelly N. Chuh
- Department of Chemistry and ‡Department of
Molecular and Computational
Biology, University of Southern California, Los Angeles, California 90089, United States
| | - Matthew R. Pratt
- Department of Chemistry and ‡Department of
Molecular and Computational
Biology, University of Southern California, Los Angeles, California 90089, United States
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Chuh K, Zaro BW, Piller F, Piller V, Pratt MR. Changes in metabolic chemical reporter structure yield a selective probe of O-GlcNAc modification. J Am Chem Soc 2014; 136:12283-95. [PMID: 25153642 PMCID: PMC4156869 DOI: 10.1021/ja504063c] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Indexed: 12/15/2022]
Abstract
Metabolic chemical reporters (MCRs) of glycosylation are analogues of monosaccharides that contain bioorthogonal functionalities and enable the direct visualization and identification of glycoproteins from living cells. Each MCR was initially thought to report on specific types of glycosylation. We and others have demonstrated that several MCRs are metabolically transformed and enter multiple glycosylation pathways. Therefore, the development of selective MCRs remains a key unmet goal. We demonstrate here that 6-azido-6-deoxy-N-acetyl-glucosamine (6AzGlcNAc) is a specific MCR for O-GlcNAcylated proteins. Biochemical analysis and comparative proteomics with 6AzGlcNAc, N-azidoacetyl-glucosamine (GlcNAz), and N-azidoacetyl-galactosamine (GalNAz) revealed that 6AzGlcNAc exclusively labels intracellular proteins, while GlcNAz and GalNAz are incorporated into a combination of intracellular and extracellular/lumenal glycoproteins. Notably, 6AzGlcNAc cannot be biosynthetically transformed into the corresponding UDP sugar-donor by the canonical salvage-pathway that requires phosphorylation at the 6-hydroxyl. In vitro experiments showed that 6AzGlcNAc can bypass this roadblock through direct phosphorylation of its 1-hydroxyl by the enzyme phosphoacetylglucosamine mutase (AGM1). Taken together, 6AzGlcNAc enables the specific analysis of O-GlcNAcylated proteins, and these results suggest that specific MCRs for other types of glycosylation can be developed. Additionally, our data demonstrate that cells are equipped with a somewhat unappreciated metabolic flexibility with important implications for the biosynthesis of natural and unnatural carbohydrates.
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Affiliation(s)
- Kelly
N. Chuh
- Department of Chemistry and Department of Molecular and Computational
Biology, University of Southern California, Los Angeles, California 90089-0744, United States
| | - Balyn W. Zaro
- Department of Chemistry and Department of Molecular and Computational
Biology, University of Southern California, Los Angeles, California 90089-0744, United States
| | - Friedrich Piller
- Centre
de Biophysique Moléculaire, CNRS UPR4301, Université d’Orléans and INSERM, F45071 Orléans
Cedex 2, France
| | - Véronique Piller
- Centre
de Biophysique Moléculaire, CNRS UPR4301, Université d’Orléans and INSERM, F45071 Orléans
Cedex 2, France
| | - Matthew R. Pratt
- Department of Chemistry and Department of Molecular and Computational
Biology, University of Southern California, Los Angeles, California 90089-0744, United States
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27
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Gurel Z, Zaro BW, Pratt MR, Sheibani N. Identification of O-GlcNAc modification targets in mouse retinal pericytes: implication of p53 in pathogenesis of diabetic retinopathy. PLoS One 2014; 9:e95561. [PMID: 24788674 PMCID: PMC4006792 DOI: 10.1371/journal.pone.0095561] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 03/28/2014] [Indexed: 12/31/2022] Open
Abstract
Hyperglycemia is the primary cause of the majority of diabetes complications, including diabetic retinopathy (DR). Hyperglycemic conditions have a detrimental effect on many tissues and cell types, especially the retinal vascular cells including early loss of pericytes (PC). However, the mechanisms behind this selective sensitivity of retinal PC to hyperglycemia are undefined. The O-linked β-N-acetylglucosamine (O-GlcNAc) modification is elevated under hyperglycemic condition, and thus, may present an important molecular modification impacting the hyperglycemia-driven complications of diabetes. We have recently demonstrated that the level of O-GlcNAc modification in response to high glucose is variable in various retinal vascular cells. Retinal PC responded with the highest increase in O-GlcNAc modification compared to retinal endothelial cells and astrocytes. Here we show that these differences translated into functional changes, with an increase in apoptosis of retinal PC, not just under high glucose but also under treatment with O-GlcNAc modification inducers, PUGNAc and Thiamet-G. To gain insight into the molecular mechanisms involved, we have used click-It chemistry and LC-MS analysis and identified 431 target proteins of O-GlcNAc modification in retinal PC using an alkynyl-modified GlcNAc analog (GlcNAlk). Among the O-GlcNAc target proteins identified here 115 of them were not previously reported to be target of O-GlcNAc modification. We have identified at least 34 of these proteins with important roles in various aspects of cell death processes. Our results indicated that increased O-GlcNAc modification of p53 was associated with an increase in its protein levels in retinal PC. Together our results suggest that post-translational O-GlcNAc modification of p53 and its increased levels may contribute to selective early loss of PC during diabetes. Thus, modulation of O-GlcNAc modification may provide a novel treatment strategy to prevent the initiation and progression of DR.
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Affiliation(s)
- Zafer Gurel
- Department of Ophthalmology and Visual Sciences, University of Wisconsin, School of Medicine and Public Health, Madison, Wisconsin, United States of America; McPherson Eye Research Institute, University of Wisconsin, School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Balyn W Zaro
- Departments of Chemistry and Molecular and Computational Biology, University of Southern California, Los Angeles, California, United States of America
| | - Matthew R Pratt
- Departments of Chemistry and Molecular and Computational Biology, University of Southern California, Los Angeles, California, United States of America
| | - Nader Sheibani
- Department of Ophthalmology and Visual Sciences, University of Wisconsin, School of Medicine and Public Health, Madison, Wisconsin, United States of America; McPherson Eye Research Institute, University of Wisconsin, School of Medicine and Public Health, Madison, Wisconsin, United States of America
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Bateman LA, Zaro BW, Miller SM, Pratt MR. An alkyne-aspirin chemical reporter for the detection of aspirin-dependent protein modification in living cells. J Am Chem Soc 2013; 135:14568-73. [PMID: 23998633 DOI: 10.1021/ja408322b] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Aspirin (acetylsalicylic acid) is widely used for the acute treatment of inflammation and the management of cardiovascular disease. More recently, it has also been shown to reduce the risk of a variety of cancers. The anti-inflammatory properties of aspirin in pain-relief, cardio-protection, and chemoprevention are well-known to result from the covalent inhibition of cyclooxygenase enzymes through nonenzymatic acetylation of key serine residues. However, any additional molecular mechanisms that may contribute to the beneficial effects of aspirin remain poorly defined. Interestingly, studies over the past 50 years using radiolabeled aspirin demonstrated that other proteins are acetylated by aspirin and enrichment with antiacetyl-lysine antibodies identified 33 potential targets of aspirin-dependent acetylation. Herein we describe the development of an alkyne-modified aspirin analogue (AspAlk) as a chemical reporters of aspirin-dependent acetylation in living cells. When combined with the Cu(I)-catalyzed [3 + 2] azide-alkyne cycloaddition, this chemical reporter allowed for the robust in-gel fluorescent detection of acetylation and the subsequent enrichment and identification of 120 proteins, 112 of which have not been previously reported to be acetylated by aspirin in cellular or in vivo contexts. Finally, AspAlk was shown to modify the core histone proteins, implicating aspirin as a potential chemical-regulator of transcription.
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Affiliation(s)
- Leslie A Bateman
- Department of Chemistry and ‡Department of Molecular and Computational Biology, University of Southern California , Los Angeles, California, United States
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29
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Abstract
Glycosylation is an abundant post-translational modification that alters the fate and function of its substrate proteins. To aid in understanding the significance of protein glycosylation, identification of target proteins is key. As with all proteomics experiments, mass spectrometry has been established as the desired method for substrate identification. However, these approaches require selective enrichment and purification of modified proteins. Chemical reporters in combination with bioorthogonal reactions have emerged as robust tools for identifying post-translational modifications including glycosylation. We provide here a method for the use of bioorthogonal chemical reporters for isolation and identification of glycosylated proteins. More specifically, this protocol is a representative procedure from our own work using an alkyne-bearing O-GlcNAc chemical reporter (GlcNAlk) and a chemically cleavable azido-azo-biotin probe for the identification of O-GlcNAc-modified proteins.
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Affiliation(s)
- Balyn W Zaro
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA
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30
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Bateman LA, Zaro BW, Chuh KN, Pratt MR. N-Propargyloxycarbamate monosaccharides as metabolic chemical reporters of carbohydrate salvage pathways and protein glycosylation. Chem Commun (Camb) 2012; 49:4328-30. [PMID: 23235740 DOI: 10.1039/c2cc37963e] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Metabolic chemical reporters of glycosylation allow for the visualization and identification of a variety of glycoconjugates by taking advantage of the promiscuity of carbohydrate metabolism. Here we describe the synthesis and characterization of metabolic chemical reporters bearing an N-propargyloxycarbamate (Poc) group that creates discrimination between glycosylation pathways.
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Affiliation(s)
- Leslie A Bateman
- Department of Chemistry, University of Southern California, Los Angeles, USA
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31
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Affiliation(s)
- Hubert D Lau
- Department of Chemistry, University of Southern California, 840 Downey Way, LJS 250, Los Angeles, CA 90089-0744, USA
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