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Cesar Ramos de Jesus H, Solis N, Machado Y, Pablos I, Bell PA, Kappelhoff R, Grin PM, Sorgi CA, Butler GS, Overall CM. Optimization of quenched fluorescent peptide substrates of SARS-CoV-2 3CL pro main protease (Mpro) from proteomic identification of P6-P6' active site specificity. J Virol 2024:e0004924. [PMID: 38742901 DOI: 10.1128/jvi.00049-24] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 04/22/2024] [Indexed: 05/16/2024] Open
Abstract
SARS-CoV-2 3C-like main protease (3CLpro) is essential for protein excision from the viral polyprotein. 3CLpro inhibitor drug development to block SARS-CoV-2 replication focuses on the catalytic non-prime (P) side for specificity and potency, but the importance of the prime (P') side in substrate specificity and for drug development remains underappreciated. We determined the P6-P6' specificity for 3CLpro from >800 cleavage sites that we identified using Proteomic Identification of Cleavage site Specificity (PICS). Cleavage occurred after the canonical P1-Gln and non-canonical P1-His and P1-Met residues. Moreover, P3 showed a preference for Arg/Lys and P3' for His. Essential H-bonds between the N-terminal Ser1 of protomer-B in 3CLpro dimers form with P1-His, but not with P1-Met. Nonetheless, cleavage occurs at P1-Met456 in native MAP4K5. Elevated reactive oxygen species in SARS-CoV-2 infection oxidize methionines. Molecular simulations revealed P1-MetOX forms an H-bond with Ser1 and notably, strong positive cooperativity between P1-Met with P3'-His was revealed, which enhanced peptide-cleavage rates. The highly plastic S3' subsite accommodates P3'-His that displays stabilizing backbone H-bonds with Thr25 lying central in a "'threonine trio" (Thr24-Thr25-Thr26) in the P'-binding domain I. Molecular docking simulations unveiled structure-activity relationships impacting 3CLpro-substrate interactions, and the role of these structural determinants was confirmed by MALDI-TOF-MS cleavage assays of P1'- and P3'-positional scanning peptide libraries carrying a 2nd optimal cut-site as an internal positive control. These data informed the design of two new and highly soluble 3CLproquenched-fluorescent peptide substrates for improved FRET monitoring of 3CLpro activity with 15× improved sensitivity over current assays.IMPORTANCEFrom global proteomics identification of >800 cleavage sites, we characterized the P6-P6' active site specificity of SARS-CoV-2 3CLpro using proteome-derived peptide library screens, molecular modeling simulations, and focussed positional peptide libraries. In P1', we show that alanine and serine are cleaved 3× faster than glycine and the hydrophobic small amino acids Leu, Ile, or Val prevent cleavage of otherwise optimal non-prime sequences. In characterizing non-canonical non-prime P1 specificity, we explored the unusual P1-Met specificity, discovering enhanced cleavage when in the oxidized state (P1-MetOX). We unveiled unexpected amino acid cooperativity at P1-Met with P3'-His and noncanonical P1-His with P2-Phe, and the importance of the threonine trio (Thr24-Thr25-Thr26) in the prime side binding domain I in defining prime side binding in SARS-CoV-2 3CLpro. From these analyses, we rationally designed quenched-fluorescence natural amino acid peptide substrates with >15× improved sensitivity and high peptide solubility, facilitating handling and application for screening of new antiviral drugs.
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Affiliation(s)
- Hugo Cesar Ramos de Jesus
- Centre for Blood Research, Life Sciences Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Nestor Solis
- Centre for Blood Research, Life Sciences Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Yoan Machado
- Centre for Blood Research, Life Sciences Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Isabel Pablos
- Centre for Blood Research, Life Sciences Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Peter A Bell
- Centre for Blood Research, Life Sciences Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Reinhild Kappelhoff
- Centre for Blood Research, Life Sciences Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Peter M Grin
- Centre for Blood Research, Life Sciences Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Carlos A Sorgi
- Centre for Blood Research, Life Sciences Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia, Canada
- Department of Chemistry, Faculty of Philosophy, Sciences and Letters at Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Georgina S Butler
- Centre for Blood Research, Life Sciences Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Christopher M Overall
- Centre for Blood Research, Life Sciences Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia, Canada
- Yonsei Frontier Lab, Yonsei University, Seoul, Republic of Korea
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Omenn GS, Lane L, Overall CM, Lindskog C, Pineau C, Packer NH, Cristea IM, Weintraub ST, Orchard S, Roehrl MHA, Nice E, Guo T, Van Eyk JE, Liu S, Bandeira N, Aebersold R, Moritz RL, Deutsch EW. The 2023 Report on the Proteome from the HUPO Human Proteome Project. J Proteome Res 2024; 23:532-549. [PMID: 38232391 PMCID: PMC11026053 DOI: 10.1021/acs.jproteome.3c00591] [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] [Indexed: 01/19/2024]
Abstract
Since 2010, the Human Proteome Project (HPP), the flagship initiative of the Human Proteome Organization (HUPO), has pursued two goals: (1) to credibly identify the protein parts list and (2) to make proteomics an integral part of multiomics studies of human health and disease. The HPP relies on international collaboration, data sharing, standardized reanalysis of MS data sets by PeptideAtlas and MassIVE-KB using HPP Guidelines for quality assurance, integration and curation of MS and non-MS protein data by neXtProt, plus extensive use of antibody profiling carried out by the Human Protein Atlas. According to the neXtProt release 2023-04-18, protein expression has now been credibly detected (PE1) for 18,397 of the 19,778 neXtProt predicted proteins coded in the human genome (93%). Of these PE1 proteins, 17,453 were detected with mass spectrometry (MS) in accordance with HPP Guidelines and 944 by a variety of non-MS methods. The number of neXtProt PE2, PE3, and PE4 missing proteins now stands at 1381. Achieving the unambiguous identification of 93% of predicted proteins encoded from across all chromosomes represents remarkable experimental progress on the Human Proteome parts list. Meanwhile, there are several categories of predicted proteins that have proved resistant to detection regardless of protein-based methods used. Additionally there are some PE1-4 proteins that probably should be reclassified to PE5, specifically 21 LINC entries and ∼30 HERV entries; these are being addressed in the present year. Applying proteomics in a wide array of biological and clinical studies ensures integration with other omics platforms as reported by the Biology and Disease-driven HPP teams and the antibody and pathology resource pillars. Current progress has positioned the HPP to transition to its Grand Challenge Project focused on determining the primary function(s) of every protein itself and in networks and pathways within the context of human health and disease.
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Affiliation(s)
- Gilbert S. Omenn
- University of Michigan, Ann Arbor, Michigan 48109, United States
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Lydie Lane
- CALIPHO Group, SIB Swiss Institute of Bioinformatics and University of Geneva, 1015 Lausanne, Switzerland
| | - Christopher M. Overall
- University of British Columbia, Vancouver, BC V6T 1Z4, Canada, Yonsei University Republic of Korea
| | | | - Charles Pineau
- University Rennes, Inserm U1085, Irset, 35042 Rennes, France
| | | | | | - Susan T. Weintraub
- University of Texas Health Science Center-San Antonio, San Antonio, Texas 78229-3900, United States
| | | | - Michael H. A. Roehrl
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, United States
| | | | - Tiannan Guo
- Westlake Center for Intelligent Proteomics, Westlake Laboratory, Westlake University, Hangzhou 310024, Zhejiang Province, China
| | - Jennifer E. Van Eyk
- Advanced Clinical Biosystems Research Institute, Smidt Heart Institute, Cedars-Sinai Medical Center, 127 South San Vicente Boulevard, Pavilion, 9th Floor, Los Angeles, CA, 90048, United States
| | - Siqi Liu
- BGI Group, Shenzhen 518083, China
| | - Nuno Bandeira
- University of California, San Diego, La Jolla, CA, 92093, United States
| | - Ruedi Aebersold
- Institute of Molecular Systems Biology in ETH Zurich, 8092 Zurich, Switzerland
- University of Zurich, 8092 Zurich, Switzerland
| | - Robert L. Moritz
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Eric W. Deutsch
- Institute for Systems Biology, Seattle, Washington 98109, United States
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Ågren MS, Hinz B, Kalogeropoulos K, Overall CM, Smola H, Werner S. Ulrich auf dem Keller (1974-2023). Wound Repair Regen 2023; 31:727-728. [PMID: 37735982 DOI: 10.1111/wrr.13118] [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] [Accepted: 09/18/2023] [Indexed: 09/23/2023]
Affiliation(s)
- Magnus S Ågren
- Department of Health and Medical Sciences, Department of Dermatology and Copenhagen Wound Healing Center, and Digestive Disease Center, University of Copenhagen, Copenhagen, Denmark
| | - Boris Hinz
- Keenan Research Institute for Biomedical Science of the St. Michael's Hospital and Faculty of Dentistry, University of Toronto, Toronto, Ontario, Canada
| | | | - Christopher M Overall
- Department of Biochemistry and Molecular Biology, Department of Oral Biological and Medical Sciences, Centre for Blood Research, University of British Columbia, Vancouver, British Columbia, Canada
| | - Hans Smola
- Health Economics and Outcome Research (HEOR) Department, HARTMANN GROUP, Heidenheim, German; Department of Dermatology, University of Cologne, Cologne, Germany
| | - Sabine Werner
- Institute of Molecular Health Sciences, Department of Biology, ETH Zurich, Zurich, Switzerland
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Coates-Park S, Lazaroff C, Gurung S, Rich J, Colladay A, O’Neill M, Butler GS, Overall CM, Stetler-Stevenson WG, Peeney D. Tissue inhibitors of metalloproteinases are proteolytic targets of matrix metalloproteinase 9. Matrix Biol 2023; 123:59-70. [PMID: 37804930 PMCID: PMC10843048 DOI: 10.1016/j.matbio.2023.09.002] [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: 07/13/2023] [Revised: 09/28/2023] [Accepted: 09/29/2023] [Indexed: 10/09/2023]
Abstract
Extracellular proteolysis and turnover are core processes of tissue homeostasis. The predominant matrix-degrading enzymes are members of the Matrix Metalloproteinase (MMP) family. MMPs extensively degrade core matrix components in addition to processing a range of other factors in the extracellular, plasma membrane, and intracellular compartments. The proteolytic activity of MMPs is modulated by the Tissue Inhibitors of Metalloproteinases (TIMPs), a family of four multi-functional matrisome proteins with extensively characterized MMP inhibitory functions. Thus, a well-regulated balance between MMP activity and TIMP levels has been described as critical for healthy tissue homeostasis, and this balance can be chronically disturbed in pathological processes. The relationship between MMPs and TIMPs is complex and lacks the constraints of a typical enzyme-inhibitor relationship due to secondary interactions between various MMPs (specifically gelatinases) and TIMP family members. We illustrate a new complexity in this system by describing how MMP9 can cleave members of the TIMP family when in molar excess. Proteolytic processing of TIMPs can generate functionally altered peptides with potentially novel attributes. We demonstrate here that all TIMPs are cleaved at their C-terminal tails by a molar excess of MMP9. This processing removes the N-glycosylation site for TIMP3 and prevents the TIMP2 interaction with latent proMMP2, a prerequisite for cell surface MMP14-mediated activation of proMMP2. TIMP2/4 are further cleaved producing ∼14 kDa N-terminal proteins linked to a smaller C-terminal domain through residual disulfide bridges. These cleaved TIMP2/4 complexes show perturbed MMP inhibitory activity, illustrating that MMP9 may bear a particularly prominent influence upon the TIMP:MMP balance in tissues.
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Affiliation(s)
- Sasha Coates-Park
- Extracellular Matrix Pathology Section, Laboratory of Pathology, National Cancer Institute, National Institute of Health, Bethesda, Maryland
| | - Carolyn Lazaroff
- Extracellular Matrix Pathology Section, Laboratory of Pathology, National Cancer Institute, National Institute of Health, Bethesda, Maryland
- Washington University in St. Louis School of Medicine, Department of Orthopedics
| | - Sadeechya Gurung
- Extracellular Matrix Pathology Section, Laboratory of Pathology, National Cancer Institute, National Institute of Health, Bethesda, Maryland
| | - Josh Rich
- Extracellular Matrix Pathology Section, Laboratory of Pathology, National Cancer Institute, National Institute of Health, Bethesda, Maryland
| | - Alexandra Colladay
- Extracellular Matrix Pathology Section, Laboratory of Pathology, National Cancer Institute, National Institute of Health, Bethesda, Maryland
| | - Maura O’Neill
- Protein Characterization Laboratory, National Cancer Institute at Frederick, National Institutes of Health, Frederick, Maryland
| | - Georgina S. Butler
- Centre for Blood Research, Life Sciences Centre, University of British Columbia; Vancouver, British Columbia, V6T 1Z3, Canada
- Department of Oral Biological and Medical Science, Faculty of Dentistry, University of British Columbia; Vancouver, British Columbia, V6T 1Z3, Canada
| | - Christopher M. Overall
- Centre for Blood Research, Life Sciences Centre, University of British Columbia; Vancouver, British Columbia, V6T 1Z3, Canada
- Department of Oral Biological and Medical Science, Faculty of Dentistry, University of British Columbia; Vancouver, British Columbia, V6T 1Z3, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia; Vancouver, British Columbia, V6T 1Z3, Canada
| | - William G. Stetler-Stevenson
- Extracellular Matrix Pathology Section, Laboratory of Pathology, National Cancer Institute, National Institute of Health, Bethesda, Maryland
| | - David Peeney
- Extracellular Matrix Pathology Section, Laboratory of Pathology, National Cancer Institute, National Institute of Health, Bethesda, Maryland
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Andrews DDT, Vlok M, Akbari Bani D, Hay BN, Mohamud Y, Foster LJ, Luo H, Overall CM, Jan E. Cleavage of 14-3-3ε by the enteroviral 3C protease dampens RIG-I-mediated antiviral signaling. J Virol 2023; 97:e0060423. [PMID: 37555661 PMCID: PMC10506458 DOI: 10.1128/jvi.00604-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 04/30/2023] [Accepted: 06/13/2023] [Indexed: 08/10/2023] Open
Abstract
Viruses have evolved diverse strategies to evade the host innate immune response and promote infection. The retinoic acid-inducible gene I (RIG-I)-like receptors RIG-I and MDA5 are antiviral factors that sense viral RNA and trigger downstream signal via mitochondrial antiviral-signaling protein (MAVS) to activate type I interferon expression. 14-3-3ε is a key component of the RIG-I translocon complex that interacts with MAVS at the mitochondrial membrane; however, the exact role of 14-3-3ε in this pathway is not well understood. In this study, we demonstrate that 14-3-3ε is a direct substrate of both the poliovirus and coxsackievirus B3 (CVB3) 3C proteases (3Cpro) and that it is cleaved at Q236↓G237, resulting in the generation of N- and C-terminal fragments of 27.0 and 2.1 kDa, respectively. While the exogenous expression of wild-type 14-3-3ε enhances IFNB mRNA production during poly(I:C) stimulation, expression of the truncated N-terminal fragment does not. The N-terminal 14-3-3ε fragment does not interact with RIG-I in co-immunoprecipitation assays, nor can it facilitate RIG-I translocation to the mitochondria. Probing the intrinsically disordered C-terminal region identifies key residues responsible for the interaction between 14-3-3ε and RIG-I. Finally, overexpression of the N-terminal fragment promotes CVB3 infection in mammalian cells. The strategic enterovirus 3Cpro-mediated cleavage of 14-3-3ε antagonizes RIG-I signaling by disrupting critical interactions within the RIG-I translocon complex, thus contributing to evasion of the host antiviral response. IMPORTANCE Host antiviral factors work to sense virus infection through various mechanisms, including a complex signaling pathway known as the retinoic acid-inducible gene I (RIG-I)-like receptor pathway. This pathway drives the production of antiviral molecules known as interferons, which are necessary to establish an antiviral state in the cellular environment. Key to this antiviral signaling pathway is the small chaperone protein 14-3-3ε, which facilitates the delivery of a viral sensor protein, RIG-I, to the mitochondria. In this study, we show that the enteroviral 3C protease cleaves 14-3-3ε during infection, rendering it incapable of facilitating this antiviral response. We also find that the resulting N-terminal cleavage fragment dampens RIG-I signaling and promotes virus infection. Our findings reveal a novel viral strategy that restricts the antiviral host response and provides insights into the mechanisms underlying 14-3-3ε function in RIG-I antiviral signaling.
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Affiliation(s)
- Daniel D. T. Andrews
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
- Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Marli Vlok
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
- Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Dorssa Akbari Bani
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
- Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Brenna N. Hay
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
- Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Yasir Mohamud
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, British Columbia, Canada
| | - Leonard J. Foster
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Honglin Luo
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, British Columbia, Canada
| | - Christopher M. Overall
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
- Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- Centre for Blood Research, University of British Columbia, Vancouver, Canada
| | - Eric Jan
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
- Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
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Bell PA, Overall CM. No Substrate Left behind-Mining of Shotgun Proteomics Datasets Rescues Evidence of Proteolysis by SARS-CoV-2 3CL pro Main Protease. Int J Mol Sci 2023; 24:ijms24108723. [PMID: 37240067 DOI: 10.3390/ijms24108723] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/11/2023] [Accepted: 05/11/2023] [Indexed: 05/28/2023] Open
Abstract
Proteolytic processing is the most ubiquitous post-translational modification and regulator of protein function. To identify protease substrates, and hence the function of proteases, terminomics workflows have been developed to enrich and detect proteolytically generated protein termini from mass spectrometry data. The mining of shotgun proteomics datasets for such 'neo'-termini, to increase the understanding of proteolytic processing, is an underutilized opportunity. However, to date, this approach has been hindered by the lack of software with sufficient speed to make searching for the relatively low numbers of protease-generated semi-tryptic peptides present in non-enriched samples viable. We reanalyzed published shotgun proteomics datasets for evidence of proteolytic processing in COVID-19 using the recently upgraded MSFragger/FragPipe software, which searches data with a speed that is an order of magnitude greater than many equivalent tools. The number of protein termini identified was higher than expected and constituted around half the number of termini detected by two different N-terminomics methods. We identified neo-N- and C-termini generated during SARS-CoV-2 infection that were indicative of proteolysis and were mediated by both viral and host proteases-a number of which had been recently validated by in vitro assays. Thus, re-analyzing existing shotgun proteomics data is a valuable adjunct for terminomics research that can be readily tapped (for example, in the next pandemic where data would be scarce) to increase the understanding of protease function and virus-host interactions, or other diverse biological processes.
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Affiliation(s)
- Peter A Bell
- Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
- Centre for Blood Research, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Christopher M Overall
- Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
- Centre for Blood Research, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
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Haack AM, Overall CM, Auf dem Keller U. Degradomics technologies in matrisome exploration. Matrix Biol 2022; 114:1-17. [PMID: 36280126 DOI: 10.1016/j.matbio.2022.10.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 10/05/2022] [Accepted: 10/20/2022] [Indexed: 11/06/2022]
Abstract
Consisting of a defined set of extracellular proteins secreted from resident cells and with minor contributions from serum proteins, the extracellular matrix (ECM) is an essential component of all tissues. Maintaining tissue homeostasis, structural support and cellular control through cell-ECM communication, the ECM has come to be viewed as not just a passive structural entity but rather as a dynamic signaling conduit between cells and the extracellular compartment. Proteins and their cleavage products mediate this communication, and aberrant signaling, either directly or indirectly distorting the ECM, results in pathological conditions including cancer, inflammation, fibrosis, and neurodegenerative diseases. Characterization of ECM components, the matrisome, the extracellular environment and their changes in disease is therefore of importance to understand and mitigate by developing novel therapeutics. Liquid chromatography-mass spectrometry (LC-MS) proteomics has been integral to protein and proteome research for decades and long superseded the obsolescent gel-based approaches. A continuous effort has ensured progress with increased sensitivity and throughput as more advanced equipment has been developed hand in hand with specialized enrichment, detection, and identification methods. Part of this effort lies in the field of degradomics, a branch of proteomics focused on discovering novel protease substrates by identification of protease-generated neo-N termini, the N-terminome, and characterizing the responsible protease networks. Various methods to do so have been developed, some specialized for specific tissue types, others for particular proteases, throughput, or ease of use. This review aims to provide an overview of the state-of-the-art proteomics techniques that have successfully been recently utilized to characterize proteolytic cleavages in the ECM and thereby guided new research and understanding of the ECM and matrisome biology.
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Affiliation(s)
- Aleksander M Haack
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, DK-2800 Kongens Lyngby, Denmark
| | - Christopher M Overall
- Department of Biochemistry and Molecular Biology, Department of Oral Biological and Medical Sciences, Centre for Blood Research, University of British Columbia, 4.401 Life Sciences Institute, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada.
| | - Ulrich Auf dem Keller
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, DK-2800 Kongens Lyngby, Denmark.
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Yates JR, Cristea IM, Dong MQ, Eyers CE, LaBaer J, Li JV, Nicholson JK, Overall CM, Palmblad M, Slavov N. Want to Publish in JPR? This Is What You Need to Know! J Proteome Res 2022; 21:2837-2839. [DOI: 10.1021/acs.jproteome.2c00704] [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: 11/16/2022]
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Omenn GS, Lane L, Overall CM, Pineau C, Packer NH, Cristea IM, Lindskog C, Weintraub ST, Orchard S, Roehrl MHA, Nice E, Liu S, Bandeira N, Chen YJ, Guo T, Aebersold R, Moritz RL, Deutsch EW. The 2022 Report on the Human Proteome from the HUPO Human Proteome Project. J Proteome Res 2022; 22:1024-1042. [PMID: 36318223 PMCID: PMC10081950 DOI: 10.1021/acs.jproteome.2c00498] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The 2022 Metrics of the Human Proteome from the HUPO Human Proteome Project (HPP) show that protein expression has now been credibly detected (neXtProt PE1 level) for 18 407 (93.2%) of the 19 750 predicted proteins coded in the human genome, a net gain of 50 since 2021 from data sets generated around the world and reanalyzed by the HPP. Conversely, the number of neXtProt PE2, PE3, and PE4 missing proteins has been reduced by 78 from 1421 to 1343. This represents continuing experimental progress on the human proteome parts list across all the chromosomes, as well as significant reclassifications. Meanwhile, applying proteomics in a vast array of biological and clinical studies continues to yield significant findings and growing integration with other omics platforms. We present highlights from the Chromosome-Centric HPP, Biology and Disease-driven HPP, and HPP Resource Pillars, compare features of mass spectrometry and Olink and Somalogic platforms, note the emergence of translation products from ribosome profiling of small open reading frames, and discuss the launch of the initial HPP Grand Challenge Project, "A Function for Each Protein".
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Affiliation(s)
- Gilbert S Omenn
- University of Michigan, Ann Arbor, Michigan48109, United States.,Institute for Systems Biology, Seattle, Washington98109, United States
| | - Lydie Lane
- CALIPHO Group, SIB Swiss Institute of Bioinformatics and University of Geneva, 1015Lausanne, Switzerland
| | | | - Charles Pineau
- French Institute of Health and Medical Research, 35042RENNESCedexFrance
| | - Nicolle H Packer
- Macquarie University, Sydney, New South Wales2109, Australia.,Griffith University's Institute for Glycomics, Sydney, New South Wales2109, Australia
| | | | | | - Susan T Weintraub
- University of Texas Health Science Center-San Antonio, San Antonio, Texas78229-3900, United States
| | - Sandra Orchard
- EMBL-EBI, Hinxton, CambridgeshireCB10 1SD, United Kingdom
| | - Michael H A Roehrl
- Memorial Sloan Kettering Cancer Center, New York, New York10065, United States
| | - Edouard Nice
- Monash University, ClaytonVictoria3800, Australia
| | - Siqi Liu
- BGI Group, Shenzhen518083, P. R. China
| | - Nuno Bandeira
- University of California, San Diego, La Jolla, California92093, United States
| | - Yu-Ju Chen
- National Taiwan University, Academia Sinica, Nankang, Taipei11529, Taiwan
| | - Tiannan Guo
- Westlake University Guomics Laboratory of Big Proteomic Data, Hangzhou310024, ZhejiangProvinceP. R. China
| | - Ruedi Aebersold
- Institute of Molecular Systems Biology in ETH Zurich, 8092Zurich, Switzerland
| | - Robert L Moritz
- Institute for Systems Biology, Seattle, Washington98109, United States
| | - Eric W Deutsch
- Institute for Systems Biology, Seattle, Washington98109, United States
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Bell PA, Scheuermann S, Renner F, Pan CL, Lu HY, Turvey SE, Bornancin F, Régnier CH, Overall CM. Integrating knowledge of protein sequence with protein function for the prediction and validation of new MALT1 substrates. Comput Struct Biotechnol J 2022; 20:4717-4732. [PMID: 36147669 PMCID: PMC9463181 DOI: 10.1016/j.csbj.2022.08.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 08/07/2022] [Accepted: 08/08/2022] [Indexed: 11/30/2022] Open
Affiliation(s)
- Peter A. Bell
- Centre for Blood Research, Life Sciences Centre, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
- Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Sophia Scheuermann
- Centre for Blood Research, Life Sciences Centre, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
- Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
- Department of Immunology, Eberhard Karl University Tübingen, 72076 Tübingen, Germany
- Department of Hematology and Oncology, University Hospital Tübingen, Children's Hospital, 72076 Tübingen, Germany
| | - Florian Renner
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
- Molecular Targeted Therapy - Discovery Oncology, Roche Pharma Research & Early Development, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
| | - Christina L. Pan
- Centre for Blood Research, Life Sciences Centre, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
- Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Henry Y. Lu
- Department of Pediatrics, British Columbia Children's Hospital, The University of British Columbia, Vancouver, BC V5Z 4H4, Canada
- Department of Experimental Medicine, Faculty of Medicine, The University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Stuart E. Turvey
- Department of Pediatrics, British Columbia Children's Hospital, The University of British Columbia, Vancouver, BC V5Z 4H4, Canada
- Department of Experimental Medicine, Faculty of Medicine, The University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Frédéric Bornancin
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Catherine H. Régnier
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Christopher M. Overall
- Centre for Blood Research, Life Sciences Centre, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
- Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
- Corresponding author at: Centre for Blood Research, Life Sciences Centre, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
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11
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Overall CM. A Flickering Light at the End of the Pandemic Tunnel. J Proteome Res 2021; 20:5223-5226. [PMID: 34856807 DOI: 10.1021/acs.jproteome.1c00866] [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: 11/30/2022]
Affiliation(s)
- Christopher M Overall
- Centre for Blood Research, Departments of Oral Biological & Medical Sciences, and Biochemistry & Molecular Biology, Faculty of Dentistry, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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12
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Drayton M, Alford MA, Pletzer D, Haney EF, Machado Y, Luo HD, Overall CM, Kizhakkedathu JN, Hancock REW, Straus SK. Enzymatically releasable polyethylene glycol - host defense peptide conjugates with improved activity and biocompatibility. J Control Release 2021; 339:220-231. [PMID: 34597746 DOI: 10.1016/j.jconrel.2021.09.035] [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] [Received: 04/20/2021] [Revised: 09/13/2021] [Accepted: 09/26/2021] [Indexed: 10/20/2022]
Abstract
Host defense peptides (HDPs) have been the subject of great interest for the treatment of multidrug-resistant bacterial infections due to their multimodal activity and low induction of resistance. However, aggregation, toxicity, and short biological half-life have limited their applicability for clinical treatment. Many methods have been explored to alleviate these issues, such as polymer (e.g., polyethylene glycol (PEG)) conjugation, but these are often accompanied by reductions in the activity of the HDP. Here, we detail the design of a novel PEG-HDP conjugate incorporating an enzymatic cleavage sequence targeting matrix metalloproteinases (MMPs) that accumulate at sites of inflammation and infection. Addition of the cleavage sequence onto either the N- or the C-terminal region of the parent peptide (peptide 73, a derivative of the HDP aurein 2.2) was explored to determine the location for optimal antimicrobial activity following MMP cleavage; furthermore, the susceptibility of the peptide to MMP cleavage after conjugation to 2 kDa or 5 kDa PEG was examined. The top candidate, L73, utilized an N-terminal cleavage site that was subsequently conjugated to a 2 kDa PEG polymer. Both L73 and the conjugate exhibited no antimicrobial activity in vitro until cleaved by purified MMP, which liberated a peptide fragment with 16- or 63-fold improved activity, respectively, corresponding to a minimum inhibitory concentration (MIC) of 8 μg/mL, comparable to that of peptide 73 (4 μg/mL). Furthermore, PEG conjugation improved the blood compatibility and reduced the aggregation tendency of the HDP in vitro, indicating enhanced biocompatibility. When administered as a single subcutaneous dose (~3.6 mg, or a peptide concentration of 142 mg/kg) in a mouse abscess model of high-density methicillin-resistant Staphylococcus aureus (MRSA) infection, the conjugate displayed strong activity, reducing abscess size and bacterial load by 73.3% and 58-fold, respectively. This activity was completely lost when the cleavage site was rendered resistant to MMPs by the substitution of two d-amino acids, supporting the hypothesis that antimicrobial activity was dependent on cleavage by MMPs, which were shown here to increasingly accumulate at the abscess site up to 18 h post infection. Finally, the conjugate displayed biocompatibility in vivo, with no identifiable toxicity or aggregation.
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Affiliation(s)
- Matthew Drayton
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada; Centre for Blood Research, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Morgan A Alford
- Centre for Blood Research, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada; Centre for Microbial Diseases and Immunity Research, Department of Microbiology and Immunology, University of British Columbia, 2259 Lower Mall Research Station, Vancouver, BC V6T 1Z4, Canada
| | - Daniel Pletzer
- Centre for Microbial Diseases and Immunity Research, Department of Microbiology and Immunology, University of British Columbia, 2259 Lower Mall Research Station, Vancouver, BC V6T 1Z4, Canada; Department of Microbiology and Immunology, University of Otago, 720 Cumberland St, Dunedin, New Zealand
| | - Evan F Haney
- Centre for Microbial Diseases and Immunity Research, Department of Microbiology and Immunology, University of British Columbia, 2259 Lower Mall Research Station, Vancouver, BC V6T 1Z4, Canada
| | - Yoan Machado
- Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Haiming D Luo
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada; Centre for Blood Research, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Christopher M Overall
- Centre for Blood Research, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Jayachandran N Kizhakkedathu
- Centre for Blood Research, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, 2350 Health Sciences Mall, Vancouver V6T 1Z3, Canada; The School of Biomedical Engineering, University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Robert E W Hancock
- Centre for Microbial Diseases and Immunity Research, Department of Microbiology and Immunology, University of British Columbia, 2259 Lower Mall Research Station, Vancouver, BC V6T 1Z4, Canada
| | - Suzana K Straus
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada.
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13
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Fung SY, Lu HY, Sharma M, Sharma AA, Saferali A, Jia A, Abraham L, Klein T, Gold MR, Noterangelo LD, Overall CM, Turvey SE. MALT1-Dependent Cleavage of HOIL1 Modulates Canonical NF-κB Signaling and Inflammatory Responsiveness. Front Immunol 2021; 12:749794. [PMID: 34721419 PMCID: PMC8552041 DOI: 10.3389/fimmu.2021.749794] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/24/2021] [Indexed: 11/13/2022] Open
Abstract
Nuclear factor kappa B (NF-κB) is a critical transcription factor involved in regulating cell activation, inflammation, and survival. The linear ubiquitin chain assembly complex (LUBAC) which consists of HOIL1, HOIP, and SHARPIN, catalyzes the linear ubiquitination of target proteins—a post-translational modification that is essential for NF-κB activation. Human germline pathogenic variants that dysregulate linear ubiquitination and NF-κB signaling are associated with immunodeficiency and/or autoinflammation including dermatitis, recurrent fevers, systemic inflammation and enteropathy. We previously identified MALT1 paracaspase as a novel negative regulator of LUBAC by proteolytic cleavage of HOIL1. To directly investigate the impact of HOIL1 cleavage activity on the inflammatory response, we employed a stable transduction system to express and directly compare non-cleavable HOIL1 with wild-type HOIL1 in primary HOIL1-deficient patient skin fibroblasts. We discovered that non-cleavable HOIL1 resulted in enhanced NF-κB signaling in response to innate stimuli. Transcriptomics revealed enrichment of inflammation and proinflammatory cytokine-related pathways after stimulation. Multiplexed cytokine assays confirmed a ‘hyperinflammatory’ phenotype in these cells. This work highlights the physiological importance of MALT1-dependent cleavage and modulation of HOIL1 on NF-κB signaling and inflammation, provides a mechanism for the autoinflammation observed in MALT1-deficient patients, and will inform the development of therapeutics that target MALT1 paracaspase and LUBAC function in treating autoinflammatory skin diseases.
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Affiliation(s)
- Shan-Yu Fung
- Department of Pediatrics, British Columbia Children's Hospital and The University of British Columbia, Vancouver, BC, Canada.,Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics and Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Henry Y Lu
- Department of Pediatrics, British Columbia Children's Hospital and The University of British Columbia, Vancouver, BC, Canada.,Experimental Medicine Program, Faculty of Medicine, The University of British Columbia, Vancouver, BC, Canada
| | - Mehul Sharma
- Department of Pediatrics, British Columbia Children's Hospital and The University of British Columbia, Vancouver, BC, Canada.,Experimental Medicine Program, Faculty of Medicine, The University of British Columbia, Vancouver, BC, Canada
| | - Ashish A Sharma
- Department of Pathology, Case Western Reserve University, Cleveland, OH, United States
| | - Aabida Saferali
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States
| | - Alicia Jia
- Department of Pediatrics, British Columbia Children's Hospital and The University of British Columbia, Vancouver, BC, Canada.,Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC, Canada
| | - Libin Abraham
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC, Canada
| | - Theo Klein
- Department of Analytical Solutions, Ducares/Triskelion BV, Utrecht, Netherlands
| | - Michael R Gold
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC, Canada
| | - Luigi D Noterangelo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Christopher M Overall
- Department of Biochemistry and Molecular Biology, Department of Oral Biological and Medical Science, Center for Blood Research, The University of British Columbia, Vancouver, BC, Canada
| | - Stuart E Turvey
- Department of Pediatrics, British Columbia Children's Hospital and The University of British Columbia, Vancouver, BC, Canada.,Experimental Medicine Program, Faculty of Medicine, The University of British Columbia, Vancouver, BC, Canada.,Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC, Canada
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14
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Pablos I, Machado Y, de Jesus HCR, Mohamud Y, Kappelhoff R, Lindskog C, Vlok M, Bell PA, Butler GS, Grin PM, Cao QT, Nguyen JP, Solis N, Abbina S, Rut W, Vederas JC, Szekely L, Szakos A, Drag M, Kizhakkedathu JN, Mossman K, Hirota JA, Jan E, Luo H, Banerjee A, Overall CM. Mechanistic insights into COVID-19 by global analysis of the SARS-CoV-2 3CL pro substrate degradome. Cell Rep 2021; 37:109892. [PMID: 34672947 PMCID: PMC8501228 DOI: 10.1016/j.celrep.2021.109892] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 09/10/2021] [Accepted: 10/05/2021] [Indexed: 12/27/2022] Open
Abstract
The main viral protease (3CLpro) is indispensable for SARS-CoV-2 replication. We delineate the human protein substrate landscape of 3CLpro by TAILS substrate-targeted N-terminomics. We identify more than 100 substrates in human lung and kidney cells supported by analyses of SARS-CoV-2-infected cells. Enzyme kinetics and molecular docking simulations of 3CLpro engaging substrates reveal how noncanonical cleavage sites, which diverge from SARS-CoV, guide substrate specificity. Cleaving the interactors of essential effector proteins, effectively stranding them from their binding partners, amplifies the consequences of proteolysis. We show that 3CLpro targets the Hippo pathway, including inactivation of MAP4K5, and key effectors of transcription, mRNA processing, and translation. We demonstrate that Spike glycoprotein directly binds galectin-8, with galectin-8 cleavage disengaging CALCOCO2/NDP52 to decouple antiviral-autophagy. Indeed, in post-mortem COVID-19 lung samples, NDP52 rarely colocalizes with galectin-8, unlike in healthy lungs. The 3CLpro substrate degradome establishes a foundational substrate atlas to accelerate exploration of SARS-CoV-2 pathology and drug design.
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Affiliation(s)
- Isabel Pablos
- Centre for Blood Research, Life Sciences Centre, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Yoan Machado
- Centre for Blood Research, Life Sciences Centre, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Hugo C Ramos de Jesus
- Centre for Blood Research, Life Sciences Centre, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Yasir Mohamud
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6Z 1Y6, Canada; Center for Heart Lung Innovation, St. Paul's Hospital, Vancouver, BC V6Z 1Y6, Canada
| | - Reinhild Kappelhoff
- Centre for Blood Research, Life Sciences Centre, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Cecilia Lindskog
- Department of Immunology Genetics and Pathology, Rudbeck Laboratory, Uppsala University, 751 85 Uppsala, Sweden
| | - Marli Vlok
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Peter A Bell
- Centre for Blood Research, Life Sciences Centre, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Georgina S Butler
- Centre for Blood Research, Life Sciences Centre, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Peter M Grin
- Centre for Blood Research, Life Sciences Centre, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Quynh T Cao
- Firestone Institute for Respiratory Health - Faculty of Health Sciences, McMaster University, Hamilton, ON L8N 4A6, Canada
| | - Jenny P Nguyen
- Firestone Institute for Respiratory Health - Faculty of Health Sciences, McMaster University, Hamilton, ON L8N 4A6, Canada
| | - Nestor Solis
- Centre for Blood Research, Life Sciences Centre, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Srinivas Abbina
- Centre for Blood Research, Life Sciences Centre, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6Z 1Y6, Canada; The School of Biomedical Engineering, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Wioletta Rut
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - John C Vederas
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Laszlo Szekely
- Department of Pathology and Cytology, Karolinska University Hospital, 141 86 Stockholm, Sweden
| | - Attila Szakos
- Department of Clinical Pathology and Cancer Diagnostics, Karolinska University Laboratories, 141 86 Stockholm, Sweden
| | - Marcin Drag
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Jayachandran N Kizhakkedathu
- Centre for Blood Research, Life Sciences Centre, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6Z 1Y6, Canada; The School of Biomedical Engineering, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Karen Mossman
- Department of Medicine, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Jeremy A Hirota
- Firestone Institute for Respiratory Health - Faculty of Health Sciences, McMaster University, Hamilton, ON L8N 4A6, Canada; Department of Medicine, McMaster University, Hamilton, ON L8S 4K1, Canada; Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada; Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Eric Jan
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Honglin Luo
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6Z 1Y6, Canada; Center for Heart Lung Innovation, St. Paul's Hospital, Vancouver, BC V6Z 1Y6, Canada
| | - Arinjay Banerjee
- Department of Medicine, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Christopher M Overall
- Centre for Blood Research, Life Sciences Centre, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
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15
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Omenn GS, Lane L, Overall CM, Paik YK, Cristea IM, Corrales FJ, Lindskog C, Weintraub S, Roehrl MHA, Liu S, Bandeira N, Srivastava S, Chen YJ, Aebersold R, Moritz RL, Deutsch EW. Progress Identifying and Analyzing the Human Proteome: 2021 Metrics from the HUPO Human Proteome Project. J Proteome Res 2021; 20:5227-5240. [PMID: 34670092 DOI: 10.1021/acs.jproteome.1c00590] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The 2021 Metrics of the HUPO Human Proteome Project (HPP) show that protein expression has now been credibly detected (neXtProt PE1 level) for 18 357 (92.8%) of the 19 778 predicted proteins coded in the human genome, a gain of 483 since 2020 from reports throughout the world reanalyzed by the HPP. Conversely, the number of neXtProt PE2, PE3, and PE4 missing proteins has been reduced by 478 to 1421. This represents remarkable progress on the proteome parts list. The utilization of proteomics in a broad array of biological and clinical studies likewise continues to expand with many important findings and effective integration with other omics platforms. We present highlights from the Immunopeptidomics, Glycoproteomics, Infectious Disease, Cardiovascular, Musculo-Skeletal, Liver, and Cancers B/D-HPP teams and from the Knowledgebase, Mass Spectrometry, Antibody Profiling, and Pathology resource pillars, as well as ethical considerations important to the clinical utilization of proteomics and protein biomarkers.
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Affiliation(s)
- Gilbert S Omenn
- University of Michigan, Ann Arbor, Michigan 48109, United States.,Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Lydie Lane
- CALIPHO Group, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | | | - Young-Ki Paik
- Yonsei Proteome Research Center and Yonsei University, Seoul 03722, Korea
| | - Ileana M Cristea
- Princeton University, Princeton, New Jersey 08544, United States
| | | | | | - Susan Weintraub
- University of Texas Health, San Antonio, San Antonio, Texas 78229-3900, United States
| | - Michael H A Roehrl
- Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Siqi Liu
- BGI Group, Shenzhen 518083, China
| | - Nuno Bandeira
- University of California, San Diego, La Jolla, California 92093, United States
| | | | - Yu-Ju Chen
- National Taiwan University, Academia Sinica, Nankang, Taipei 11529, Taiwan
| | - Ruedi Aebersold
- ETH-Zurich and University of Zurich, 8092 Zurich, Switzerland
| | - Robert L Moritz
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Eric W Deutsch
- Institute for Systems Biology, Seattle, Washington 98109, United States
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16
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Juurikka K, Dufour A, Pehkonen K, Mainoli B, Campioni Rodrigues P, Solis N, Klein T, Nyberg P, Overall CM, Salo T, Åström P. MMP8 increases tongue carcinoma cell-cell adhesion and diminishes migration via cleavage of anti-adhesive FXYD5. Oncogenesis 2021; 10:44. [PMID: 34059618 PMCID: PMC8167110 DOI: 10.1038/s41389-021-00334-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 03/17/2021] [Revised: 05/03/2021] [Accepted: 05/14/2021] [Indexed: 12/28/2022] Open
Abstract
Matrix metalloproteinases (MMPs) modify bioactive factors via selective processing or degradation resulting in tumour-promoting or tumour-suppressive effects, such as those by MMP8 in various cancers. We mapped the substrates of MMP8 to elucidate its previously shown tumour-protective role in oral tongue squamous cell carcinoma (OTSCC). MMP8 overexpressing (+) HSC-3 cells, previously demonstrated to have reduced migration and invasion, showed enhanced cell-cell adhesion. By analysing the secretomes of MMP8 + and control cells with terminal amine isotopic labelling of substrates (TAILS) coupled with liquid chromatography and tandem mass spectrometry (LC-MS/MS), we identified 36 potential substrates of MMP8, including FXYD domain-containing ion transport regulator 5 (FXYD5). An anti-adhesive glycoprotein FXYD5 has been previously shown to predict poor survival in OTSCC. Cleavage of FXYD5 by MMP8 was confirmed using recombinant proteins. Furthermore, we detected a loss of FXYD5 levels on cell membrane of MMP8 + cells, which was rescued by inhibition of the proteolytic activity of MMP8. Silencing (si) FXYD5 increased the cell-cell adhesion of control but not that of MMP8 + cells. siFXYD5 diminished the viability and motility of HSC-3 cells independent of MMP8 and similar effects were seen in another tongue cancer cell line, SCC-25. FXYD5 is a novel substrate of MMP8 and reducing FXYD5 levels either with siRNA or cleavage by MMP8 increases cell adhesion leading to reduced motility. FXYD5 being a known prognostic factor in OTSCC, our findings strengthen its potential as a therapeutic target.
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Affiliation(s)
- K Juurikka
- Cancer and Translational Medicine Research Unit, Faculty of Medicine, University of Oulu, Oulu, Finland.,Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - A Dufour
- Department of Physiology & Pharmacology, University of Calgary, Calgary, Canada.,Department of Oral Biological and Medical Sciences, Faculty of Dentistry, Centre for Blood Research, and Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada
| | - K Pehkonen
- Cancer and Translational Medicine Research Unit, Faculty of Medicine, University of Oulu, Oulu, Finland.,Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - B Mainoli
- Department of Physiology & Pharmacology, University of Calgary, Calgary, Canada
| | - P Campioni Rodrigues
- Cancer and Translational Medicine Research Unit, Faculty of Medicine, University of Oulu, Oulu, Finland.,Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - N Solis
- Department of Oral Biological and Medical Sciences, Faculty of Dentistry, Centre for Blood Research, and Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada
| | - T Klein
- Department of Oral Biological and Medical Sciences, Faculty of Dentistry, Centre for Blood Research, and Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada
| | - P Nyberg
- Cancer and Translational Medicine Research Unit, Faculty of Medicine, University of Oulu, Oulu, Finland.,Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland.,Biobank Borealis of Northern Finland, Oulu University Hospital, Oulu, Finland
| | - C M Overall
- Department of Oral Biological and Medical Sciences, Faculty of Dentistry, Centre for Blood Research, and Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada
| | - T Salo
- Cancer and Translational Medicine Research Unit, Faculty of Medicine, University of Oulu, Oulu, Finland.,Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland.,Department of Oral and Maxillofacial Diseases, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Helsinki University Hospital, Helsinki, Finland.,Translational Immunology Research Program (TRIMM), University of Helsinki, Helsinki, Finland
| | - P Åström
- Cancer and Translational Medicine Research Unit, Faculty of Medicine, University of Oulu, Oulu, Finland. .,Department of Oral Biological and Medical Sciences, Faculty of Dentistry, Centre for Blood Research, and Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada. .,Research Unit of Biomedicine, Faculty of Medicine, University of Oulu, Oulu, Finland.
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17
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Alcaraz LB, Mallavialle A, David T, Derocq D, Delolme F, Dieryckx C, Mollevi C, Boissière-Michot F, Simony-Lafontaine J, Du Manoir S, Huesgen PF, Overall CM, Tartare-Deckert S, Jacot W, Chardès T, Guiu S, Roger P, Reinheckel T, Moali C, Liaudet-Coopman E. A 9-kDa matricellular SPARC fragment released by cathepsin D exhibits pro-tumor activity in the triple-negative breast cancer microenvironment. Am J Cancer Res 2021; 11:6173-6192. [PMID: 33995652 PMCID: PMC8120228 DOI: 10.7150/thno.58254] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 03/20/2021] [Indexed: 12/26/2022] Open
Abstract
Rationale: Alternative therapeutic strategies based on tumor-specific molecular targets are urgently needed for triple-negative breast cancer (TNBC). The protease cathepsin D (cath-D) is a marker of poor prognosis in TNBC and a tumor-specific extracellular target for antibody-based therapy. The identification of cath-D substrates is crucial for the mechanistic understanding of its role in the TNBC microenvironment and future therapeutic developments. Methods: The cath-D substrate repertoire was investigated by N-Terminal Amine Isotopic Labeling of Substrates (TAILS)-based degradome analysis in a co-culture assay of TNBC cells and breast fibroblasts. Substrates were validated by amino-terminal oriented mass spectrometry of substrates (ATOMS). Cath-D and SPARC expression in TNBC was examined using an online transcriptomic survival analysis, tissue micro-arrays, TNBC cell lines, patient-derived xenografts (PDX), human TNBC samples, and mammary tumors from MMTV-PyMT Ctsd-/-knock-out mice. The biological role of SPARC and its fragments in TNBC were studied using immunohistochemistry and immunofluorescence analysis, gene expression knockdown, co-culture assays, western blot analysis, RT-quantitative PCR, adhesion assays, Transwell motility, trans-endothelial migration and invasion assays. Results: TAILS analysis showed that the matricellular protein SPARC is a substrate of extracellular cath-D. In vitro, cath-D induced limited proteolysis of SPARC C-terminal extracellular Ca2+ binding domain at acidic pH, leading to the production of SPARC fragments (34-, 27-, 16-, 9-, and 6-kDa). Similarly, cath-D secreted by TNBC cells cleaved fibroblast- and cancer cell-derived SPARC at the tumor pericellular acidic pH. SPARC cleavage also occurred in TNBC tumors. Among these fragments, only the 9-kDa SPARC fragment inhibited TNBC cell adhesion and spreading on fibronectin, and stimulated their migration, endothelial transmigration, and invasion. Conclusions: Our study establishes a novel crosstalk between proteases and matricellular proteins in the tumor microenvironment through limited SPARC proteolysis, revealing a novel targetable 9-kDa bioactive SPARC fragment for new TNBC treatments. Our study will pave the way for the development of strategies for targeting bioactive fragments from matricellular proteins in TNBC.
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Tam V, Chen P, Yee A, Solis N, Klein T, Kudelko M, Sharma R, Chan WC, Overall CM, Haglund L, Sham PC, Cheah KSE, Chan D. DIPPER, a spatiotemporal proteomics atlas of human intervertebral discs for exploring ageing and degeneration dynamics. eLife 2020; 9:64940. [PMID: 33382035 PMCID: PMC7857729 DOI: 10.7554/elife.64940] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [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: 11/16/2020] [Accepted: 12/30/2020] [Indexed: 12/11/2022] Open
Abstract
The spatiotemporal proteome of the intervertebral disc (IVD) underpins its integrity and function. We present DIPPER, a deep and comprehensive IVD proteomic resource comprising 94 genome-wide profiles from 17 individuals. To begin with, protein modules defining key directional trends spanning the lateral and anteroposterior axes were derived from high-resolution spatial proteomes of intact young cadaveric lumbar IVDs. They revealed novel region-specific profiles of regulatory activities and displayed potential paths of deconstruction in the level- and location-matched aged cadaveric discs. Machine learning methods predicted a ‘hydration matrisome’ that connects extracellular matrix with MRI intensity. Importantly, the static proteome used as point-references can be integrated with dynamic proteome (SILAC/degradome) and transcriptome data from multiple clinical samples, enhancing robustness and clinical relevance. The data, findings, and methodology, available on a web interface (http://www.sbms.hku.hk/dclab/DIPPER/), will be valuable references in the field of IVD biology and proteomic analytics. The backbone of vertebrate animals consists of a series of bones called vertebrae that are joined together by disc-like structures that allow the back to move and distribute forces to protect it during daily activities. It is common for these intervertebral discs to degenerate with age, resulting in back pain and severely reducing quality of life. The mechanical features of intervertebral discs are the result of their proteins. These include extracellular matrix proteins, which form the external scaffolding that binds cells together in a tissue, and signaling proteins, which allow cells to communicate. However, how the levels of different proteins in each region of the disc vary with time has not been fully examined. To establish how protein composition changes with age, Tam, Chen et al. quantified the protein levels and gene activity (which leads to protein production) of intervertebral discs from young and old deceased individuals. They found that the position of different mixtures of proteins in the intervertebral disc changes with age, and that young people have high levels of extracellular matrix proteins and signaling proteins. Levels of these proteins decreased as people got older, as did the amount of proteins produced. To determine which region of the intervertebral disc different proteins were in, Tam, Chen et al. also performed magnetic resonance imaging (MRI) of the samples to correlate image intensity (which represents water content) with the corresponding protein signature. The data obtained provides a high-quality map of how the location of different proteins changes with age, and is available online under the name DIPPER. This database is an informative resource for research into skeletal biology, and it will likely advance the understanding of intervertebral disc degeneration in humans and animals, potentially leading to the development of new treatment strategies for this condition.
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Affiliation(s)
- Vivian Tam
- School of Biomedical Sciences,, The University of Hong Kong, Hong Kong.,The University of Hong Kong Shenzhen of Research Institute and Innovation (HKU-SIRI), Shenzhen, China
| | - Peikai Chen
- School of Biomedical Sciences,, The University of Hong Kong, Hong Kong
| | - Anita Yee
- School of Biomedical Sciences,, The University of Hong Kong, Hong Kong
| | - Nestor Solis
- Centre for Blood Research, Faculty of Dentistry, University of British Columbia, Vancouver, Canada
| | - Theo Klein
- Centre for Blood Research, Faculty of Dentistry, University of British Columbia, Vancouver, Canada
| | - Mateusz Kudelko
- School of Biomedical Sciences,, The University of Hong Kong, Hong Kong
| | - Rakesh Sharma
- Proteomics and Metabolomics Core Facility, The University of Hong Kong, Hong Kong
| | - Wilson Cw Chan
- School of Biomedical Sciences,, The University of Hong Kong, Hong Kong.,The University of Hong Kong Shenzhen of Research Institute and Innovation (HKU-SIRI), Shenzhen, China.,Department of Orthopaedics Surgery and Traumatology, HKU-Shenzhen Hospital, Shenzhen, China
| | - Christopher M Overall
- Centre for Blood Research, Faculty of Dentistry, University of British Columbia, Vancouver, Canada
| | - Lisbet Haglund
- Department of Surgery, McGill University, Montreal, Canada
| | - Pak C Sham
- Centre for PanorOmic Sciences (CPOS), The University of Hong Kong, Hong Kong
| | | | - Danny Chan
- School of Biomedical Sciences,, The University of Hong Kong, Hong Kong.,The University of Hong Kong Shenzhen of Research Institute and Innovation (HKU-SIRI), Shenzhen, China
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Affiliation(s)
- Christopher M Overall
- Centre for Blood Research, Departments of Oral Biological & Medical Sciences, and Biochemistry & Molecular Biology, Faculty of Dentistry, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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20
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Affiliation(s)
- Christopher M Overall
- Centre for Blood Research, Departments of Oral Biological & Medical Sciences and Biochemistry & Molecular Biology, Faculty of Dentistry, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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21
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Omenn GS, Lane L, Overall CM, Cristea IM, Corrales FJ, Lindskog C, Paik YK, Van Eyk JE, Liu S, Pennington SR, Snyder MP, Baker MS, Bandeira N, Aebersold R, Moritz RL, Deutsch EW. Research on the Human Proteome Reaches a Major Milestone: >90% of Predicted Human Proteins Now Credibly Detected, According to the HUPO Human Proteome Project. J Proteome Res 2020; 19:4735-4746. [PMID: 32931287 DOI: 10.1021/acs.jproteome.0c00485] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
According to the 2020 Metrics of the HUPO Human Proteome Project (HPP), expression has now been detected at the protein level for >90% of the 19 773 predicted proteins coded in the human genome. The HPP annually reports on progress made throughout the world toward credibly identifying and characterizing the complete human protein parts list and promoting proteomics as an integral part of multiomics studies in medicine and the life sciences. NeXtProt release 2020-01 classified 17 874 proteins as PE1, having strong protein-level evidence, up 180 from 17 694 one year earlier. These represent 90.4% of the 19 773 predicted coding genes (all PE1,2,3,4 proteins in neXtProt). Conversely, the number of neXtProt PE2,3,4 proteins, termed the "missing proteins" (MPs), was reduced by 230 from 2129 to 1899 since the neXtProt 2019-01 release. PeptideAtlas is the primary source of uniform reanalysis of raw mass spectrometry data for neXtProt, supplemented this year with extensive data from MassIVE. PeptideAtlas 2020-01 added 362 canonical proteins between 2019 and 2020 and MassIVE contributed 84 more, many of which converted PE1 entries based on non-MS evidence to the MS-based subgroup. The 19 Biology and Disease-driven B/D-HPP teams continue to pursue the identification of driver proteins that underlie disease states, the characterization of regulatory mechanisms controlling the functions of these proteins, their proteoforms, and their interactions, and the progression of transitions from correlation to coexpression to causal networks after system perturbations. And the Human Protein Atlas published Blood, Brain, and Metabolic Atlases.
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Affiliation(s)
- Gilbert S Omenn
- University of Michigan, Ann Arbor, Michigan 48109, United States.,Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Lydie Lane
- CALIPHO Group, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | | | - Ileana M Cristea
- Princeton University, Princeton, New Jersey 08544, United States
| | | | | | | | | | - Siqi Liu
- BGI Group, Shenzhen 518083, China
| | | | | | - Mark S Baker
- Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Nuno Bandeira
- University of California, San Diego, La Jolla, California 92093, United States
| | - Ruedi Aebersold
- ETH-Zurich and University of Zurich, 8092 Zurich, Switzerland
| | - Robert L Moritz
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Eric W Deutsch
- Institute for Systems Biology, Seattle, Washington 98109, United States
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22
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Adhikari S, Nice EC, Deutsch EW, Lane L, Omenn GS, Pennington SR, Paik YK, Overall CM, Corrales FJ, Cristea IM, Van Eyk JE, Uhlén M, Lindskog C, Chan DW, Bairoch A, Waddington JC, Justice JL, LaBaer J, Rodriguez H, He F, Kostrzewa M, Ping P, Gundry RL, Stewart P, Srivastava S, Srivastava S, Nogueira FCS, Domont GB, Vandenbrouck Y, Lam MPY, Wennersten S, Vizcaino JA, Wilkins M, Schwenk JM, Lundberg E, Bandeira N, Marko-Varga G, Weintraub ST, Pineau C, Kusebauch U, Moritz RL, Ahn SB, Palmblad M, Snyder MP, Aebersold R, Baker MS. A high-stringency blueprint of the human proteome. Nat Commun 2020; 11:5301. [PMID: 33067450 PMCID: PMC7568584 DOI: 10.1038/s41467-020-19045-9] [Citation(s) in RCA: 122] [Impact Index Per Article: 30.5] [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: 12/19/2019] [Accepted: 09/25/2020] [Indexed: 02/07/2023] Open
Abstract
The Human Proteome Organization (HUPO) launched the Human Proteome Project (HPP) in 2010, creating an international framework for global collaboration, data sharing, quality assurance and enhancing accurate annotation of the genome-encoded proteome. During the subsequent decade, the HPP established collaborations, developed guidelines and metrics, and undertook reanalysis of previously deposited community data, continuously increasing the coverage of the human proteome. On the occasion of the HPP's tenth anniversary, we here report a 90.4% complete high-stringency human proteome blueprint. This knowledge is essential for discerning molecular processes in health and disease, as we demonstrate by highlighting potential roles the human proteome plays in our understanding, diagnosis and treatment of cancers, cardiovascular and infectious diseases.
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Affiliation(s)
- Subash Adhikari
- Faculty of Medicine, Health and Human Sciences, Department of Biomedical Sciences, Macquarie University, North Ryde, NSW, 2109, Australia
| | - Edouard C Nice
- Faculty of Medicine, Health and Human Sciences, Department of Biomedical Sciences, Macquarie University, North Ryde, NSW, 2109, Australia
- Faculty of Medicine, Nursing and Health Sciences, Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, 3800, Australia
| | - Eric W Deutsch
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA, 98109, USA
| | - Lydie Lane
- Faculty of Medicine, SIB-Swiss Institute of Bioinformatics and Department of Microbiology and Molecular Medicine, University of Geneva, CMU, Michel-Servet 1, 1211, Geneva, Switzerland
| | - Gilbert S Omenn
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109-2218, USA
| | - Stephen R Pennington
- UCD Conway Institute of Biomolecular and Biomedical Research, School of Medicine, University College Dublin, Dublin, Ireland
| | - Young-Ki Paik
- Yonsei Proteome Research Center, 50 Yonsei-ro, Sudaemoon-ku, Seoul, 120-749, South Korea
| | | | - Fernando J Corrales
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología-CSIC, Proteored-ISCIII, 28049, Madrid, Spain
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Jennifer E Van Eyk
- Cedars Sinai Medical Center, Advanced Clinical Biosystems Research Institute, The Smidt Heart Institute, Los Angeles, CA, 90048, USA
| | - Mathias Uhlén
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 17121, Solna, Sweden
| | - Cecilia Lindskog
- Rudbeck Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, 75185, Uppsala, Sweden
| | - Daniel W Chan
- Department of Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21224, USA
| | - Amos Bairoch
- Faculty of Medicine, SIB-Swiss Institute of Bioinformatics and Department of Microbiology and Molecular Medicine, University of Geneva, CMU, Michel-Servet 1, 1211, Geneva, Switzerland
| | - James C Waddington
- UCD Conway Institute of Biomolecular and Biomedical Research, School of Medicine, University College Dublin, Dublin, Ireland
| | - Joshua L Justice
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Joshua LaBaer
- Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Fuchu He
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Markus Kostrzewa
- Bruker Daltonik GmbH, Microbiology and Diagnostics, Fahrenheitstrasse, 428359, Bremen, Germany
| | - Peipei Ping
- Cardiac Proteomics and Signaling Laboratory, Department of Physiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Rebekah L Gundry
- CardiOmics Program, Center for Heart and Vascular Research, Division of Cardiovascular Medicine and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Peter Stewart
- Department of Chemical Pathology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | | | - Sudhir Srivastava
- Cancer Biomarkers Research Branch, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Suite 5E136, Rockville, MD, 20852, USA
| | - Fabio C S Nogueira
- Proteomics Unit and Laboratory of Proteomics, Institute of Chemistry, Federal University of Rio de Janeiro, Av Athos da Silveria Ramos, 149, 21941-909, Rio de Janeiro, RJ, Brazil
| | - Gilberto B Domont
- Proteomics Unit and Laboratory of Proteomics, Institute of Chemistry, Federal University of Rio de Janeiro, Av Athos da Silveria Ramos, 149, 21941-909, Rio de Janeiro, RJ, Brazil
| | - Yves Vandenbrouck
- University of Grenoble Alpes, Inserm, CEA, IRIG-BGE, U1038, 38000, Grenoble, France
| | - Maggie P Y Lam
- Departments of Medicine-Cardiology and Biochemistry and Molecular Genetics, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
- Consortium for Fibrosis Research and Translation, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Sara Wennersten
- Division of Cardiology, Department of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Juan Antonio Vizcaino
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Marc Wilkins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Jochen M Schwenk
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 17121, Solna, Sweden
| | - Emma Lundberg
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 17121, Solna, Sweden
| | - Nuno Bandeira
- Department of Computer Science and Engineering, University of California, San Diego, 9500 Gilman Drive, Mail Code 0404, La Jolla, CA, 92093-0404, USA
| | | | - Susan T Weintraub
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center San Antonio, UT Health, 7703 Floyd Curl Drive, San Antonio, TX, 78229-3900, USA
| | - Charles Pineau
- University of Rennes, Inserm, EHESP, IREST, UMR_S 1085, F-35042, Rennes, France
| | - Ulrike Kusebauch
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA, 98109, USA
| | - Robert L Moritz
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA, 98109, USA
| | - Seong Beom Ahn
- Faculty of Medicine, Health and Human Sciences, Department of Biomedical Sciences, Macquarie University, North Ryde, NSW, 2109, Australia
| | - Magnus Palmblad
- Leiden University Medical Center, Leiden, 2333, The Netherlands
| | - Michael P Snyder
- Department of Genetics, Stanford School of Medicine, Stanford, CA, 94305, USA
| | - Ruedi Aebersold
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA, 98109, USA
- Faculty of Science, University of Zurich, Zurich, Switzerland
| | - Mark S Baker
- Faculty of Medicine, Health and Human Sciences, Department of Biomedical Sciences, Macquarie University, North Ryde, NSW, 2109, Australia.
- Department of Genetics, Stanford School of Medicine, Stanford, CA, 94305, USA.
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23
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Affiliation(s)
- Young-Ki Paik
- Yonsei Proteome Research Center, College of Life Science and Technology , Yonsei University
| | - Christopher M Overall
- Centre for Blood Research, Departments of Oral Biological & Medical Sciences and Biochemistry & Molecular Biology, Faculty of Dentistry , University of British Columbia
| | - Fernando Corrales
- Functional Proteomics Laboratory National Center of Biotechnology , CSIC
| | | | - Lydie Lane
- CALIPHO Group, SIB Swiss Institute of Bioinformatics and Department of Microbiology and Molecular Medicine, Faculty of Medicine, CMU , University of Geneva
| | - Gilbert S Omenn
- Institute for Systems Biology, Departments of Computational Medicine & Bioinformatics, Internal Medicine, and Human Genetics & School of Public Health , University of Michigan
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24
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Minina EA, Staal J, Alvarez VE, Berges JA, Berman-Frank I, Beyaert R, Bidle KD, Bornancin F, Casanova M, Cazzulo JJ, Choi CJ, Coll NS, Dixit VM, Dolinar M, Fasel N, Funk C, Gallois P, Gevaert K, Gutierrez-Beltran E, Hailfinger S, Klemenčič M, Koonin EV, Krappmann D, Linusson A, Machado MFM, Madeo F, Megeney LA, Moschou PN, Mottram JC, Nyström T, Osiewacz HD, Overall CM, Pandey KC, Ruland J, Salvesen GS, Shi Y, Smertenko A, Stael S, Ståhlberg J, Suárez MF, Thome M, Tuominen H, Van Breusegem F, van der Hoorn RAL, Vardi A, Zhivotovsky B, Lam E, Bozhkov PV. Classification and Nomenclature of Metacaspases and Paracaspases: No More Confusion with Caspases. Mol Cell 2020; 77:927-929. [PMID: 32142688 PMCID: PMC7325697 DOI: 10.1016/j.molcel.2019.12.020] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 12/16/2019] [Accepted: 12/23/2019] [Indexed: 01/19/2023]
Affiliation(s)
- Elena A Minina
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden; COS, Heidelberg University, Heidelberg, Germany.
| | - Jens Staal
- VIB Center for Inflammation Research, Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Vanina E Alvarez
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martin, San Martin, Buenos Aires, Argentina
| | - John A Berges
- Department of Biological Sciences and School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Ilana Berman-Frank
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Israel
| | - Rudi Beyaert
- VIB Center for Inflammation Research, Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Kay D Bidle
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, USA
| | | | - Magali Casanova
- Aix-Marseille Univ, CNRS, LISM, Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Juan J Cazzulo
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martin, San Martin, Buenos Aires, Argentina
| | - Chang Jae Choi
- The University of Texas at Austin, Marine Science Institute, Port Aransas, TX, USA
| | - Nuria S Coll
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain
| | - Vishva M Dixit
- Department of Physiological Chemistry, Genentech, South San Francisco, CA, USA
| | - Marko Dolinar
- University of Ljubljana, Faculty of Chemistry and Chemical Technology, Ljubljana, Slovenia
| | - Nicolas Fasel
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland
| | | | - Patrick Gallois
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Kris Gevaert
- VIB Center for Medical Biotechnology, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Emilio Gutierrez-Beltran
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla and Consejo Superior de Investigaciones Científicas, Sevilla, Spain
| | - Stephan Hailfinger
- Interfaculty Institute for Biochemistry, Eberhard Karls University, Tübingen, Germany
| | - Marina Klemenčič
- University of Ljubljana, Faculty of Chemistry and Chemical Technology, Ljubljana, Slovenia
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, USA
| | - Daniel Krappmann
- Research Unit Cellular Signal Integration, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Anna Linusson
- Department of Chemistry, Umeå University, Umeå, Sweden
| | - Maurício F M Machado
- Interdisciplinary Center for Biochemical Research, University of Mogi das Cruzes, Mogi das Cruzes, Brazil
| | - Frank Madeo
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, BioTechMed Graz, Graz, Austria
| | - Lynn A Megeney
- Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute and Departments of Medicine and Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Panagiotis N Moschou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Heraklion, Greece; Department of Biology, University of Crete, Greece; Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Jeremy C Mottram
- York Biomedical Research Institute, Department of Biology, University of York, York, UK
| | - Thomas Nyström
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health - AgeCap, University of Gothenburg, Gothenburg, Sweden
| | - Heinz D Osiewacz
- Institute for Molecular Biosciences, Faculty of Biosciences, Goethe University, Frankfurt/Main, Germany
| | - Christopher M Overall
- Departments of Oral Biological and Medical Sciences and Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - Kailash C Pandey
- Protein Biochemistry and Engineering Laboratory, ICMR-National Institute of Malaria Research, New Delhi, India
| | - Jürgen Ruland
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany; German Cancer Consortium (DKTK), partner site Munich, Germany; German Center for Infection Research (DZIF), partner site Munich, Germany
| | - Guy S Salvesen
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Yigong Shi
- School of Life Sciences, Westlake University, Xihu District, Hangzhou Zhejiang Province, China
| | - Andrei Smertenko
- Institute of Biological Chemistry, Washington State University, Pullman, WA, USA
| | - Simon Stael
- VIB Center for Medical Biotechnology, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
| | - Jerry Ståhlberg
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - María Fernanda Suárez
- Departamento de Biologia Molecular y Bioquimica, Facultad de Ciencias, Universidad de Malaga, Campus de Teatinos, Malaga, Spain
| | - Margot Thome
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland
| | - Hannele Tuominen
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
| | | | - Assaf Vardi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Boris Zhivotovsky
- Division of Toxicology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden; Faculty of Fundamental Medicine, MV Lomonosov Moscow State University, Moscow, Russia
| | - Eric Lam
- Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, NJ USA
| | - Peter V Bozhkov
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden.
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25
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Omenn GS, Lane L, Overall CM, Corrales FJ, Schwenk JM, Paik YK, Van Eyk JE, Liu S, Pennington S, Snyder MP, Baker MS, Deutsch EW. Progress on Identifying and Characterizing the Human Proteome: 2019 Metrics from the HUPO Human Proteome Project. J Proteome Res 2019; 18:4098-4107. [PMID: 31430157 PMCID: PMC6898754 DOI: 10.1021/acs.jproteome.9b00434] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [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: 01/17/2023]
Abstract
The Human Proteome Project (HPP) annually reports on progress made throughout the field in credibly identifying and characterizing the complete human protein parts list and making proteomics an integral part of multiomics studies in medicine and the life sciences. NeXtProt release 2019-01-11 contains 17 694 proteins with strong protein-level evidence (PE1), compliant with HPP Guidelines for Interpretation of MS Data v2.1; these represent 89% of all 19 823 neXtProt predicted coding genes (all PE1,2,3,4 proteins), up from 17 470 one year earlier. Conversely, the number of neXtProt PE2,3,4 proteins, termed the "missing proteins" (MPs), has been reduced from 2949 to 2129 since 2016 through efforts throughout the community, including the chromosome-centric HPP. PeptideAtlas is the source of uniformly reanalyzed raw mass spectrometry data for neXtProt; PeptideAtlas added 495 canonical proteins between 2018 and 2019, especially from studies designed to detect hard-to-identify proteins. Meanwhile, the Human Protein Atlas has released version 18.1 with immunohistochemical evidence of expression of 17 000 proteins and survival plots as part of the Pathology Atlas. Many investigators apply multiplexed SRM-targeted proteomics for quantitation of organ-specific popular proteins in studies of various human diseases. The 19 teams of the Biology and Disease-driven B/D-HPP published a total of 160 publications in 2018, bringing proteomics to a broad array of biomedical research.
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Affiliation(s)
- Gilbert S. Omenn
- Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, Michigan 48109-2218, United States
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109-5263, United States
| | - Lydie Lane
- CALIPHO Group, SIB Swiss Institute of Bioinformatics and Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, CMU, Michel-Servet 1, 1211 Geneva 4, Switzerland
| | - Christopher M. Overall
- Life Sciences Institute, Faculty of Dentistry, University of British Columbia, 2350 Health Sciences Mall, Room 4.401, Vancouver, British Columbia V6T 1Z3, Canada
| | | | - Jochen M. Schwenk
- Science for Life Laboratory, KTH Royal Institute of Technology, Tomtebodavägen 23A, 17165 Solna, Sweden
| | - Young-Ki Paik
- Yonsei Proteome Research Center, Yonsei University, Room 425, Building #114, 50 Yonsei-ro, Seodaemoon-ku, Seoul 120-749, South Korea
| | - Jennifer E. Van Eyk
- Advanced Clinical BioSystems Research Institute, Cedars Sinai Precision Biomarker Laboratories, Barbra Streisand Women’s Heart Center, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Siqi Liu
- BGI Group-Shenzhen, Yantian District, Shenzhen 518083, China
| | - Stephen Pennington
- School of Medicine, University College Dublin, Conway Institute Belfield, Dublin 4, Ireland
| | - Michael P. Snyder
- Department of Genetics, Stanford University, Alway Building, 300 Pasteur Drive and 3165 Porter Drive, Palo Alto, California 94304, United States
| | - Mark S. Baker
- Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, 75 Talavera Road, North Ryde, NSW 2109, Australia
| | - Eric W. Deutsch
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109-5263, United States
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Jobin PG, Solis N, Machado Y, Bell PA, Rai SK, Kwon NH, Kim S, Overall CM, Butler GS. Moonlighting matrix metalloproteinase substrates: Enhancement of proinflammatory functions of extracellular tyrosyl-tRNA synthetase upon cleavage. J Biol Chem 2019; 295:2186-2202. [PMID: 31771979 PMCID: PMC7039567 DOI: 10.1074/jbc.ra119.010486] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [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: 08/02/2019] [Revised: 11/03/2019] [Indexed: 12/19/2022] Open
Abstract
Tyrosyl-tRNA synthetase ligates tyrosine to its cognate tRNA in the cytoplasm, but it can also be secreted through a noncanonical pathway. We found that extracellular tyrosyl-tRNA synthetase (YRS) exhibited proinflammatory activities. In addition to acting as a monocyte/macrophage chemoattractant, YRS initiated signaling through Toll-like receptor 2 (TLR2) resulting in NF-κB activation and release of tumor necrosis factor α (TNFα) and multiple chemokines, including MIP-1α/β, CXCL8 (IL8), and CXCL1 (KC) from THP1 monocyte and peripheral blood mononuclear cell–derived macrophages. Furthermore, YRS up-regulated matrix metalloproteinase (MMP) activity in a TNFα-dependent manner in M0 macrophages. Because MMPs process a variety of intracellular proteins that also exhibit extracellular moonlighting functions, we profiled 10 MMPs for YRS cleavage and identified 55 cleavage sites by amino-terminal oriented mass spectrometry of substrates (ATOMS) positional proteomics and Edman degradation. Stable proteoforms resulted from cleavages near the start of the YRS C-terminal EMAPII domain. All of the MMPs tested cleaved at ADS386↓387LYV and VSG405↓406LVQ, generating 43- and 45-kDa fragments. The highest catalytic efficiency for YRS was demonstrated by MMP7, which is highly expressed by monocytes and macrophages, and by neutrophil-specific MMP8. MMP-cleaved YRS enhanced TLR2 signaling, increased TNFα secretion from macrophages, and amplified monocyte/macrophage chemotaxis compared with unprocessed YRS. The cleavage of YRS by MMP8, but not MMP7, was inhibited by tyrosine, a substrate of the YRS aminoacylation reaction. Overall, the proinflammatory activity of YRS is enhanced by MMP cleavage, which we suggest forms a feed-forward mechanism to promote inflammation.
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Affiliation(s)
- Parker G Jobin
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada; Centre for Blood Research, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Nestor Solis
- Centre for Blood Research, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Yoan Machado
- Centre for Blood Research, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Peter A Bell
- Centre for Blood Research, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Simran K Rai
- Centre for Blood Research, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada; Graduate Program in Bioinformatics, University of British Columbia, Vancouver, British Columbia V5T 4S6, Canada
| | - Nam Hoon Kwon
- College of Pharmacy, Seoul National University, 151-742, Seoul, Republic of Korea; Medicinal Bioconvergence Research Center, Seoul National University, 151-742, Seoul, Republic of Korea
| | - Sunghoon Kim
- College of Pharmacy, Seoul National University, 151-742, Seoul, Republic of Korea; Medicinal Bioconvergence Research Center, Seoul National University, 151-742, Seoul, Republic of Korea
| | - Christopher M Overall
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada; Centre for Blood Research, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.
| | - Georgina S Butler
- Centre for Blood Research, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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Deutsch EW, Lane L, Overall CM, Bandeira N, Baker MS, Pineau C, Moritz RL, Corrales F, Orchard S, Van Eyk JE, Paik YK, Weintraub ST, Vandenbrouck Y, Omenn GS. Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 3.0. J Proteome Res 2019; 18:4108-4116. [PMID: 31599596 DOI: 10.1021/acs.jproteome.9b00542] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Human Proteome Organization's (HUPO) Human Proteome Project (HPP) developed Mass Spectrometry (MS) Data Interpretation Guidelines that have been applied since 2016. These guidelines have helped ensure that the emerging draft of the complete human proteome is highly accurate and with low numbers of false-positive protein identifications. Here, we describe an update to these guidelines based on consensus-reaching discussions with the wider HPP community over the past year. The revised 3.0 guidelines address several major and minor identified gaps. We have added guidelines for emerging data independent acquisition (DIA) MS workflows and for use of the new Universal Spectrum Identifier (USI) system being developed by the HUPO Proteomics Standards Initiative (PSI). In addition, we discuss updates to the standard HPP pipeline for collecting MS evidence for all proteins in the HPP, including refinements to minimum evidence. We present a new plan for incorporating MassIVE-KB into the HPP pipeline for the next (HPP 2020) cycle in order to obtain more comprehensive coverage of public MS data sets. The main checklist has been reorganized under headings and subitems, and related guidelines have been grouped. In sum, Version 2.1 of the HPP MS Data Interpretation Guidelines has served well, and this timely update to version 3.0 will aid the HPP as it approaches its goal of collecting and curating MS evidence of translation and expression for all predicted ∼20 000 human proteins encoded by the human genome.
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Affiliation(s)
- Eric W Deutsch
- Institute for Systems Biology , Seattle , Washington 98109 , United States
| | - Lydie Lane
- SIB Swiss Institute of Bioinformatics and Department of Microbiology and Molecular Medicine, Faculty of Medicine , University of Geneva , CMU, Michel Servet 1 , 1211 Geneva 4 , Switzerland
| | - Christopher M Overall
- Centre for Blood Research, Departments of Oral Biological & Medical Sciences, and Biochemistry & Molecular Biology, Faculty of Dentistry , The University of British Columbia , Vancouver , BC V6T 1Z4 , Canada
| | - Nuno Bandeira
- Center for Computational Mass Spectrometry and Department of Computer Science and Engineering, Skaggs School of Pharmacy and Pharmaceutical Sciences , University of California San Diego , La Jolla , California 92093 , United States
| | - Mark S Baker
- Department of Biomedical Sciences, Faculty of Medicine and Health Science , Macquarie University , Macquarie Park , NSW 2109 , Australia
| | - Charles Pineau
- Univ. Rennes , Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail) - UMR_S 1085 , F-35042 Rennes cedex , France
| | - Robert L Moritz
- Institute for Systems Biology , Seattle , Washington 98109 , United States
| | - Fernando Corrales
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología , Spanish Research Council , ProteoRed-.ISCIII , Madrid 117 , Spain
| | - Sandra Orchard
- European Molecular Biology Laboratory , European Bioinformatics Institute (EMBL-EBI) , Wellcome Trust Genome Campus , Hinxton , Cambridge CB10 1SD , U.K
| | - Jennifer E Van Eyk
- Advanced Clinical Biosystems Research Institute, The Smidt Heart Institute, Department of Medicine , Cedars Sinai Medical Center , Los Angeles , California 90048 , United States
| | - Young-Ki Paik
- Yonsei Proteome Research Center , Yonsei University , 50 Yonsei-ro , Sudaemoon-ku , Seoul 03720 , Korea
| | - Susan T Weintraub
- The University of Texas Health Science Center at San Antonio , San Antonio , Texas 78229 , United States
| | - Yves Vandenbrouck
- Univ. Grenoble Alpes , CEA, INSERM, IRIG-BGE, U1038 , F-38000 Grenoble , France
| | - Gilbert S Omenn
- Institute for Systems Biology , Seattle , Washington 98109 , United States.,Departments of Computational Medicine & Bioinformatics, Internal Medicine, and Human Genetics and School of Public Health , University of Michigan , Ann Arbor , Michigan 48109-2218 , United States
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28
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Paik YK, Overall CM, Corrales F, Deutsch EW, Lane L, Omenn GS. Toward Completion of the Human Proteome Parts List: Progress Uncovering Proteins That Are Missing or Have Unknown Function and Developing Analytical Methods. J Proteome Res 2019; 17:4023-4030. [PMID: 30985145 PMCID: PMC6288998 DOI: 10.1021/acs.jproteome.8b00885] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Young-Ki Paik
- Yonsei Proteome Research Center, College of Life Science and Technology, Yonsei University
| | - Christopher M Overall
- Centre for Blood Research, Departments of Oral Biological & Medical Sciences and Biochemistry & Molecular Biology, Faculty of Dentistry, University of British Columbia
| | - Fernando Corrales
- Functional Proteomics Laboratory National Center of Biotechnology, CSIC
| | | | - Lydie Lane
- CALIPHO Group, SIB Swiss Institute of Bioinformatics and Department of Microbiology and Molecular Medicine, Faculty of Medicine, CMU, University of Geneva
| | - Gilbert S Omenn
- Institute for Systems Biology, Departments of Computational Medicine & Bioinformatics, Internal Medicine, and Human Genetics & School of Public Health, University of Michigan
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Bell PA, Solis N, Kizhakkedathu JN, Matthew I, Overall CM. Proteomic and N-Terminomic TAILS Analyses of Human Alveolar Bone Proteins: Improved Protein Extraction Methodology and LysargiNase Digestion Strategies Increase Proteome Coverage and Missing Protein Identification. J Proteome Res 2019; 18:4167-4179. [DOI: 10.1021/acs.jproteome.9b00445] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Ehrhardt K, Steck N, Kappelhoff R, Stein S, Rieder F, Gordon IO, Boyle EC, Braubach P, Overall CM, Finlay BB, Grassl GA. Persistent Salmonella enterica Serovar Typhimurium Infection Induces Protease Expression During Intestinal Fibrosis. Inflamm Bowel Dis 2019; 25:1629-1643. [PMID: 31066456 PMCID: PMC6749888 DOI: 10.1093/ibd/izz070] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Indexed: 12/15/2022]
Abstract
BACKGROUND Intestinal fibrosis is a common and serious complication of Crohn's disease characterized by the accumulation of fibroblasts, deposition of extracellular matrix, and formation of scar tissue. Although many factors including cytokines and proteases contribute to the development of intestinal fibrosis, the initiating mechanisms and the complex interplay between these factors remain unclear. METHODS Chronic infection of mice with Salmonella enterica serovar Typhimurium was used to induce intestinal fibrosis. A murine protease-specific CLIP-CHIP microarray analysis was employed to assess regulation of proteases and protease inhibitors. To confirm up- or downregulation during fibrosis, we performed quantitative real-time polymerase chain reaction (PCR) and immunohistochemical stainings in mouse tissue and tissue from patients with inflammatory bowel disease. In vitro infections were used to demonstrate a direct effect of bacterial infection in the regulation of proteases. RESULTS Mice develop severe and persistent intestinal fibrosis upon chronic infection with Salmonella enterica serovar Typhimurium, mimicking the pathology of human disease. Microarray analyses revealed 56 up- and 40 downregulated proteases and protease inhibitors in fibrotic cecal tissue. Various matrix metalloproteases, serine proteases, cysteine proteases, and protease inhibitors were regulated in the fibrotic tissue, 22 of which were confirmed by quantitative real-time PCR. Proteases demonstrated site-specific staining patterns in intestinal fibrotic tissue from mice and in tissue from human inflammatory bowel disease patients. Finally, we show in vitro that Salmonella infection directly induces protease expression in macrophages and epithelial cells but not in fibroblasts. CONCLUSIONS In summary, we show that chronic Salmonella infection regulates proteases and protease inhibitors during tissue fibrosis in vivo and in vitro, and therefore this model is well suited to investigating the role of proteases in intestinal fibrosis.
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Affiliation(s)
- Katrin Ehrhardt
- Institute of Medical Microbiology and Hospital Epidemiology and German Center for Infection Research (DZIF), Partner Site Hannover, Hannover Medical School, Hannover, Germany
| | - Natalie Steck
- Institute for Experimental Medicine, Christian-Albrechts University of Kiel, Kiel, Germany, and Research Center Borstel, Borstel, Germany
| | - Reinhild Kappelhoff
- Department of Oral Biological and Medical Sciences, Centre for Blood Research, Faculty of Dentistry, University of British Columbia, Vancouver, BC, Canada
| | - Stephanie Stein
- Institute for Experimental Medicine, Christian-Albrechts University of Kiel, Kiel, Germany, and Research Center Borstel, Borstel, Germany,Present affiliation: Center for Internal Medicine, I. Medical Clinic and Polyclinic, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Florian Rieder
- Department of Gastroenterology, Hepatology and Nutrition, Digestive Diseases and Surgery Institute
| | - Ilyssa O Gordon
- Department of Pathology, Pathology and Laboratory Medicine Institute, Cleveland Clinic Foundation, Cleveland, Ohio, USA
| | - Erin C Boyle
- Department of Cardiothoracic, Transplantation, and Vascular Surgery, Hannover Medical School, Hannover, Germany,Institute for Laboratory Animal Science, Hannover Medical School, Hannover, Germany
| | - Peter Braubach
- Institute for Pathology, Hannover Medical School, Hannover, Germany
| | - Christopher M Overall
- Department of Oral Biological and Medical Sciences, Centre for Blood Research, Faculty of Dentistry, University of British Columbia, Vancouver, BC, Canada
| | - B Brett Finlay
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Guntram A Grassl
- Institute of Medical Microbiology and Hospital Epidemiology and German Center for Infection Research (DZIF), Partner Site Hannover, Hannover Medical School, Hannover, Germany,Address correspondence to: Guntram A. Grassl, PhD, Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany ()
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Solis N, Parambath A, Abbina S, Kizhakkedathu J, Overall CM. Simplified high yield TAILS terminomics using a new HPG-ALD 800K-2000 polymer with precipitation. Methods Enzymol 2019; 626:429-446. [PMID: 31606086 DOI: 10.1016/bs.mie.2019.07.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [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: 01/07/2023]
Abstract
Identification of the N terminus of proteins in complex samples has been accelerated in recent years by the increased power of mass spectrometers, bioinformatic tools and biochemical methods. We developed Terminal Amine Isotopic Labeling of Substrates (TAILS), a powerful method for the isolation, identification and quantification of N terminal peptides comprising the N terminome from proteome in vitro analyses, cultured cells and tissues. TAILS depletes internal tryptic peptides so enriching for the natural and cleaved neo N-terminal peptides present in complex proteome samples. To do so N-terminal peptides are blocked at the protein level by isotopically labeled amine reactive reagents, then digested with trypsin. TAILS relies on a water-soluble 100-kDa highly-branched polyglycerol polymer (HPG-ALD) developed in our laboratories to bind and deplete the sample of tryptic peptides. Polymer-bound internal tryptic peptides are separated from the blocked N-terminal peptides by spin filters. Here we describe a revised TAILS protocol that uses a newly developed 800-kDa HPG-ALD polymer that allows precipitation of the polymer post-depletion. Precipitation has multiple advantages over spin filters including maximal N-terminal peptide recovery and faster high-throughput N-terminome identification and quantification in any sample type.
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Affiliation(s)
- Nestor Solis
- Centre for Blood Research, University of British Columbia, Vancouver, BC, Canada; Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC, Canada
| | - Anilkumar Parambath
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Srinivas Abbina
- Centre for Blood Research, University of British Columbia, Vancouver, BC, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Jayachandran Kizhakkedathu
- Centre for Blood Research, University of British Columbia, Vancouver, BC, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada; Department of Chemistry, University of British Columbia, Vancouver, BC, Canada
| | - Christopher M Overall
- Centre for Blood Research, University of British Columbia, Vancouver, BC, Canada; Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC, Canada; Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, BC, Canada.
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Zelanis A, Oliveira AK, Prudova A, Huesgen PF, Tashima AK, Kizhakkedathu J, Overall CM, Serrano SMT. Deep Profiling of the Cleavage Specificity and Human Substrates of Snake Venom Metalloprotease HF3 by Proteomic Identification of Cleavage Site Specificity (PICS) Using Proteome Derived Peptide Libraries and Terminal Amine Isotopic Labeling of Substrates (TAILS) N-Terminomics. J Proteome Res 2019; 18:3419-3428. [PMID: 31337208 DOI: 10.1021/acs.jproteome.9b00325] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Snakebite is a major medical concern in many parts of the world with metalloproteases playing important roles in the pathological effects of Viperidae venoms, including local tissue damage, hemorrhage, and coagulopathy. Hemorrhagic Factor 3 (HF3), a metalloprotease from Bothrops jararaca venom, induces local hemorrhage and targets extracellular matrix (ECM) components, including collagens and proteoglycans, and plasma proteins. However, the full substrate repertoire of this metalloprotease is unknown. We report positional proteomic studies identifying >2000 N-termini, including neo-N-termini of HF3 cleavage sites in mouse embryonic fibroblast secretome proteins. Terminal amine isotopic labeling of substrates (TAILS) analysis identified a preference for Leu at the P1' position among candidate HF3 substrates including proteins of the ECM and focal adhesions and the cysteine protease inhibitor cystatin-C. Interestingly, 190 unique peptides matched to annotated cleavage sites in the TopFIND N-termini database, suggesting that these cleavages occurred at a site prone to cleavage or might have been generated by other proteases activated upon incubation with HF3, including caspases-3 and -7, cathepsins D and E, granzyme B, and MMPs 2 and 9. Using Proteomic identification of cleavage site specificity (PICS), a tryptic library derived from THP-1 monocytic cells was used as HF3 substrates for identifying protease cleavage sites and sequence preferences in peptides. A total of 799 unique cleavage sites were detected and, in accordance with TAILS analysis using native secreted protein substrates of MEF cells, revealed a clear preference for Leu at P1'. Taken together, these results greatly expand the known substrate degradome of HF3 and reveal potential new targets, which may serve as a basis to better elucidate the complex pathophysiology of snake envenomation.
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Affiliation(s)
- André Zelanis
- Department of Science and Technology , Federal University of São Paulo (ICT-UNIFESP) , São José dos Campos , SP 12231-280 , Brazil.,Laboratório Especial de Toxinologia Aplicada, Center of Toxins, Immune-Response and Cell Signaling (CeTICS) , Instituto Butantan , São Paulo , SP 05503-000 , Brazil
| | - Ana K Oliveira
- Laboratório Especial de Toxinologia Aplicada, Center of Toxins, Immune-Response and Cell Signaling (CeTICS) , Instituto Butantan , São Paulo , SP 05503-000 , Brazil
| | - Anna Prudova
- Centre for Blood Research , University of British Columbia , Vancouver , BC V6T 1Z3 , Canada.,Department of Oral Biological and Medical Sciences, Faculty of Dentistry , University of British Columbia , Vancouver , BC V6T 1Z3 , Canada
| | - Pitter F Huesgen
- Centre for Blood Research , University of British Columbia , Vancouver , BC V6T 1Z3 , Canada.,Central Institute for Engineering, Electronics and Analytics, ZEA-3 , Forschungszentrum Jülich , Juelich 52425 , Germany
| | - Alexandre K Tashima
- Laboratório Especial de Toxinologia Aplicada, Center of Toxins, Immune-Response and Cell Signaling (CeTICS) , Instituto Butantan , São Paulo , SP 05503-000 , Brazil
| | - Jayachandran Kizhakkedathu
- Centre for Blood Research , University of British Columbia , Vancouver , BC V6T 1Z3 , Canada.,Department of Pathology and Laboratory Medicine , University of British Columbia , Vancouver , BC V6T 1Z3 , Canada
| | - Christopher M Overall
- Centre for Blood Research , University of British Columbia , Vancouver , BC V6T 1Z3 , Canada.,Department of Oral Biological and Medical Sciences, Faculty of Dentistry , University of British Columbia , Vancouver , BC V6T 1Z3 , Canada
| | - Solange M T Serrano
- Laboratório Especial de Toxinologia Aplicada, Center of Toxins, Immune-Response and Cell Signaling (CeTICS) , Instituto Butantan , São Paulo , SP 05503-000 , Brazil
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Chopra S, Overall CM, Dufour A. Matrix metalloproteinases in the CNS: interferons get nervous. Cell Mol Life Sci 2019; 76:3083-3095. [PMID: 31165203 PMCID: PMC11105576 DOI: 10.1007/s00018-019-03171-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 05/22/2019] [Accepted: 05/29/2019] [Indexed: 12/14/2022]
Abstract
Matrix metalloproteinases (MMPs) have been investigated in context of chronic inflammatory diseases and demonstrated to degrade multiple components of the extracellular matrix (ECM). However, following several disappointing MMP clinical trials, recent studies have demonstrated unexpected novel functions of MMPs in viral infections and autoimmune inflammatory diseases in unanticipated locations. Thus, MMPs play additional functions in inflammation than just ECM degradation. They can regulate the activity of chemokines and cytokines of the immune response by precise proteolytic processing resulting in activation or inactivation of signaling pathways. MMPs have been demonstrated to cleave multiple substrates of the central nervous systems (CNS) and contribute to promoting and dampening diseases of the CNS. Initially, believed to be solely promoting pathologies, more than 10 MMPs to date have been shown to have protective functions. Here, we present some of the beneficial and destructive roles of MMPs in CNS pathologies and discuss strategies for the use of MMP inhibitors.
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Affiliation(s)
- Sameeksha Chopra
- Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada
- McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Christopher M Overall
- Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
- Centre for Blood Research, Vancouver, BC, V6T 1Z3, Canada
| | - Antoine Dufour
- Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada.
- McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, AB, T2N 4N1, Canada.
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34
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Jobin PG, Solis N, Machado Y, Bell PA, Kwon NH, Kim S, Overall CM, Butler GS. Matrix metalloproteinases inactivate the proinflammatory functions of secreted moonlighting tryptophanyl-tRNA synthetase. J Biol Chem 2019; 294:12866-12879. [PMID: 31324718 DOI: 10.1074/jbc.ra119.009584] [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: 05/30/2019] [Revised: 07/11/2019] [Indexed: 01/08/2023] Open
Abstract
Tryptophanyl-tRNA synthetase (WRS) is a cytosolic aminoacyl-tRNA synthetase essential for protein synthesis. WRS is also one of a growing number of intracellular proteins that are attributed distinct noncanonical "moonlighting" functions in the extracellular milieu. Moonlighting aminoacyl-tRNA synthetases regulate processes such as inflammation, but how these multifunctional enzymes are themselves regulated remains unclear. Here, we demonstrate that WRS is secreted from human macrophages, fibroblasts, and endothelial cells in response to the proinflammatory cytokine interferon γ (IFNγ). WRS signaled primarily through Toll-like receptor 2 (TLR2) in macrophages, leading to phosphorylation of the p65 subunit of NF-κB with associated loss of NF-κB inhibitor α (IκB-α) protein. This signaling initiated secretion of tumor necrosis factor α (TNFα) and CXCL8 (IL8) from macrophages. We also demonstrated that WRS is a potent monocyte chemoattractant. Of note, WRS increased matrix metalloproteinase (MMP) activity in the conditioned medium of macrophages in a TNFα-dependent manner. Using purified recombinant proteins and LC-MS/MS to identify proteolytic cleavage sites, we demonstrated that multiple MMPs, but primarily macrophage MMP7 and neutrophil MMP8, cleave secreted WRS at several sites. Loss of the WHEP domain following cleavage at Met48 generated a WRS proteoform that also results from alternative splicing, designated Δ1-47 WRS. The MMP-cleaved WRS lacked TLR signaling and proinflammatory activities. Thus, our results suggest that moonlighting WRS promotes IFNγ proinflammatory activities, and these responses can be dampened by MMPs.
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Affiliation(s)
- Parker G Jobin
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada; Centre for Blood Research, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada
| | - Nestor Solis
- Centre for Blood Research, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, University of British Columbia, 2199 Wesbrook Mall, Faculty of Dentistry, Vancouver, British Columbia V6T 1Z3, Canada
| | - Yoan Machado
- Centre for Blood Research, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, University of British Columbia, 2199 Wesbrook Mall, Faculty of Dentistry, Vancouver, British Columbia V6T 1Z3, Canada
| | - Peter A Bell
- Centre for Blood Research, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, University of British Columbia, 2199 Wesbrook Mall, Faculty of Dentistry, Vancouver, British Columbia V6T 1Z3, Canada
| | - Nam Hoon Kwon
- College of Pharmacy, Seoul National University, 151-742 Seoul, Republic of Korea; Medicinal Bioconvergance Research Center, Seoul National University, 151-742 Seoul, Republic of Korea
| | - Sunghoon Kim
- College of Pharmacy, Seoul National University, 151-742 Seoul, Republic of Korea; Medicinal Bioconvergance Research Center, Seoul National University, 151-742 Seoul, Republic of Korea
| | - Christopher M Overall
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada; Centre for Blood Research, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, University of British Columbia, 2199 Wesbrook Mall, Faculty of Dentistry, Vancouver, British Columbia V6T 1Z3, Canada.
| | - Georgina S Butler
- Centre for Blood Research, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, University of British Columbia, 2199 Wesbrook Mall, Faculty of Dentistry, Vancouver, British Columbia V6T 1Z3, Canada
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Lee J, Vinh NB, Drinkwater N, Yang W, Kannan Sivaraman K, Schembri LS, Gazdik M, Grin PM, Butler GS, Overall CM, Charman SA, McGowan S, Scammells PJ. Novel Human Aminopeptidase N Inhibitors: Discovery and Optimization of Subsite Binding Interactions. J Med Chem 2019; 62:7185-7209. [PMID: 31251594 DOI: 10.1021/acs.jmedchem.9b00757] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Aminopeptidase N (APN/CD13) is a zinc-dependent M1 aminopeptidase that contributes to cancer progression by promoting angiogenesis, metastasis, and tumor invasion. We have previously identified hydroxamic acid-containing analogues that are potent inhibitors of the APN homologue from the malarial parasite Plasmodium falciparum M1 aminopeptidase (PfA-M1). Herein, we describe the rationale that underpins the repurposing of PfA-M1 inhibitors as novel APN inhibitors. A series of novel hydroxamic acid analogues were developed using a structure-based design approach and evaluated their inhibition activities against APN. N-(2-(Hydroxyamino)-2-oxo-1-(3',4',5'-trifluoro-[1,1'-biphenyl]-4-yl)ethyl)-4-(methylsulfonamido)benzamide (6ad) proved to be an extremely potent inhibitor of APN activity in vitro, selective against other zinc-dependent enzymes such as matrix metalloproteases, and possessed limited cytotoxicity against Ad293 cells and favorable physicochemical and metabolic stability properties. The combined results indicate that compound 6ad may be a useful lead for the development of anticancer agents.
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Affiliation(s)
| | | | - Nyssa Drinkwater
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology , Monash University , Clayton Campus , Clayton , VIC 3800 , Australia
| | - Wei Yang
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology , Monash University , Clayton Campus , Clayton , VIC 3800 , Australia
| | - Komagal Kannan Sivaraman
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology , Monash University , Clayton Campus , Clayton , VIC 3800 , Australia
| | | | | | | | | | | | | | - Sheena McGowan
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology , Monash University , Clayton Campus , Clayton , VIC 3800 , Australia
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36
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Trudel D, Avarvarei LM, Orain M, Turcotte S, Plante M, Grégoire J, Kappelhoff R, Labbé DP, Bachvarov D, Têtu B, Overall CM, Bairati I. Proteases and their inhibitors as prognostic factors for high-grade serous ovarian cancer. Pathol Res Pract 2019; 215:152369. [PMID: 30987833 DOI: 10.1016/j.prp.2019.02.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 02/21/2019] [Accepted: 02/26/2019] [Indexed: 01/30/2023]
Abstract
Ovarian carcinoma is one of the most lethal malignancies, but only very few prognostic biomarkers are known. The degradome, comprising proteases, protease non-proteolytic homologues and inhibitors, have been involved in the prognosis of many cancer types, including ovarian carcinoma. The prognostic significance of the whole degradome family has not been specifically studied in high-grade serous ovarian cancer. A targeted DNA microarray known as the CLIP-CHIP microarray was used to identify potential prognostic factors in ten high-grade serous ovarian cancer women who had early recurrence (<1.6 years) or late/no recurrence after first line surgery and chemotherapy. In women with early recurrence, we identified seven upregulated genes (TMPRSS4, MASP1/3, SPC18, PSMB1, IGFBP2, CFI - encoding Complement Factor I - and MMP9) and one down-regulated gene (ADAM-10). Using immunohistochemistry, we evaluated the prognostic effect of these 8 candidate genes in an independent cohort of 112 high-grade serous ovarian cancer women. Outcomes were progression, defined according to CA-125 criteria, and death. Multivariate Cox proportional hazard regression models were done to estimate the associations between each protein and each outcome. High ADAM-10 expression (intensity of 2-3) was associated with a lower risk of progression (adjusted hazard ratio (HR): 0.51; 95% confidence interval (CI): 0.29-0.87). High complement factor I expression (intensity 2-3) was associated with a higher risk of progression (adjusted HR: 2.30, 95% CI: 1.17-4.53) and death (adjusted HR: 3.42; 95% CI: 1.72-6.79). Overall, we identified the prognostic value of two proteases, ADAM-10 and complement factor I, for high-grade serous ovarian cancer which could have clinical significance.
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Affiliation(s)
- Dominique Trudel
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM)/ Institut du cancer de Montréal, Montréal, QC, H2X 0A9, Canada; Department of Pathology, Centre Hospitalier de l'Université de Montréal, Montréal, QC, H2X 3O4, Canada; Department of Pathology and Cellular Biology, Faculty of Medicine, Université de Montréal, Montréal, QC, H3T 1J4, Canada; Laval University Cancer Research Center and Research Center of the Centre Hospitalier Universitaire (CHU) de Québec, Ville de Québec, QC, G1R 3S3, Canada.
| | - Luminita-Mihaela Avarvarei
- Laval University Cancer Research Center and Research Center of the Centre Hospitalier Universitaire (CHU) de Québec, Ville de Québec, QC, G1R 3S3, Canada
| | - Michèle Orain
- Laval University Cancer Research Center and Research Center of the Centre Hospitalier Universitaire (CHU) de Québec, Ville de Québec, QC, G1R 3S3, Canada
| | - Stéphane Turcotte
- Laval University Cancer Research Center and Research Center of the Centre Hospitalier Universitaire (CHU) de Québec, Ville de Québec, QC, G1R 3S3, Canada
| | - Marie Plante
- Laval University Cancer Research Center and Research Center of the Centre Hospitalier Universitaire (CHU) de Québec, Ville de Québec, QC, G1R 3S3, Canada; Gynecologic Oncology Division, Centre Hospitalier Universitaire (CHU) de Québec, Québec, QC, G1R 2J6, Canada
| | - Jean Grégoire
- Laval University Cancer Research Center and Research Center of the Centre Hospitalier Universitaire (CHU) de Québec, Ville de Québec, QC, G1R 3S3, Canada; Gynecologic Oncology Division, Centre Hospitalier Universitaire (CHU) de Québec, Québec, QC, G1R 2J6, Canada
| | - Reinhild Kappelhoff
- Centre for Blood Research, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences and Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - David P Labbé
- Department of Surgery, Division of Urology, Faculty of Medicine, McGill University, Montréal, QC, H3A 0G4, Canada
| | - Dimcho Bachvarov
- Laval University Cancer Research Center and Research Center of the Centre Hospitalier Universitaire (CHU) de Québec, Ville de Québec, QC, G1R 3S3, Canada
| | - Bernard Têtu
- Laval University Cancer Research Center and Research Center of the Centre Hospitalier Universitaire (CHU) de Québec, Ville de Québec, QC, G1R 3S3, Canada; Anatomic Pathology and Cytology Department, Hôpital du St-Sacrement, Centre Hospitalier Universitaire de Québec, Laval University, Québec, QC, G1S 4L8, Canada
| | - Christopher M Overall
- Centre for Blood Research, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences and Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Isabelle Bairati
- Laval University Cancer Research Center and Research Center of the Centre Hospitalier Universitaire (CHU) de Québec, Ville de Québec, QC, G1R 3S3, Canada
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Yang H, Li YC, Zhao MZ, Wu FL, Wang X, Xiao WD, Wang YH, Zhang JL, Wang FQ, Xu F, Zeng WF, Overall CM, He SM, Chi H, Xu P. Precision De Novo Peptide Sequencing Using Mirror Proteases of Ac-LysargiNase and Trypsin for Large-scale Proteomics. Mol Cell Proteomics 2019; 18:773-785. [PMID: 30622160 PMCID: PMC6442358 DOI: 10.1074/mcp.tir118.000918] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Revised: 11/20/2018] [Indexed: 11/06/2022] Open
Abstract
De novo peptide sequencing for large-scale proteomics remains challenging because of the lack of full coverage of ion series in tandem mass spectra. We developed a mirror protease of trypsin, acetylated LysargiNase (Ac-LysargiNase), with superior activity and stability. The mirror spectrum pairs derived from the Ac-LysargiNase and trypsin treated samples can generate full b and y ion series, which provide mutual complementarity of each other, and allow us to develop a novel algorithm, pNovoM, for de novo sequencing. Using pNovoM to sequence peptides of purified proteins, the accuracy of the sequence was close to 100%. More importantly, from a large-scale yeast proteome sample digested with trypsin and Ac-LysargiNase individually, 48% of all tandem mass spectra formed mirror spectrum pairs, 97% of which contained full coverage of ion series, resulting in precision de novo sequencing of full-length peptides by pNovoM. This enabled pNovoM to successfully sequence 21,249 peptides from 3,753 proteins and interpreted 44-152% more spectra than pNovo+ and PEAKS at a 5% FDR at the spectrum level. Moreover, the mirror protease strategy had an obvious advantage in sequencing long peptides. We believe that the combination of mirror protease strategy and pNovoM will be an effective approach for precision de novo sequencing on both single proteins and proteome samples.
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Affiliation(s)
- Hao Yang
- From the ‡Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS; University of Chinese Academy of Sciences; Institute of Computing Technology, CAS, Beijing 100190, China
| | - Yan-Chang Li
- §State Key Laboratory of Proteomics; Beijing Proteome Research Center; National Center for Protein Sciences Beijing; Beijing Institute of Lifeomics, Beijing 102206, China
| | - Ming-Zhi Zhao
- §State Key Laboratory of Proteomics; Beijing Proteome Research Center; National Center for Protein Sciences Beijing; Beijing Institute of Lifeomics, Beijing 102206, China
| | - Fei-Lin Wu
- §State Key Laboratory of Proteomics; Beijing Proteome Research Center; National Center for Protein Sciences Beijing; Beijing Institute of Lifeomics, Beijing 102206, China
| | - Xi Wang
- From the ‡Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS; University of Chinese Academy of Sciences; Institute of Computing Technology, CAS, Beijing 100190, China
| | - Wei-Di Xiao
- §State Key Laboratory of Proteomics; Beijing Proteome Research Center; National Center for Protein Sciences Beijing; Beijing Institute of Lifeomics, Beijing 102206, China
| | - Yi-Hao Wang
- §State Key Laboratory of Proteomics; Beijing Proteome Research Center; National Center for Protein Sciences Beijing; Beijing Institute of Lifeomics, Beijing 102206, China
| | - Jun-Ling Zhang
- §State Key Laboratory of Proteomics; Beijing Proteome Research Center; National Center for Protein Sciences Beijing; Beijing Institute of Lifeomics, Beijing 102206, China
| | - Fu-Qiang Wang
- §State Key Laboratory of Proteomics; Beijing Proteome Research Center; National Center for Protein Sciences Beijing; Beijing Institute of Lifeomics, Beijing 102206, China
| | - Feng Xu
- §State Key Laboratory of Proteomics; Beijing Proteome Research Center; National Center for Protein Sciences Beijing; Beijing Institute of Lifeomics, Beijing 102206, China
| | - Wen-Feng Zeng
- From the ‡Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS; University of Chinese Academy of Sciences; Institute of Computing Technology, CAS, Beijing 100190, China
| | - Christopher M Overall
- ‖Centre for Blood Research, University of British Columbia, Vancouver, British Columbia, Canada
| | - Si-Min He
- From the ‡Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS; University of Chinese Academy of Sciences; Institute of Computing Technology, CAS, Beijing 100190, China;.
| | - Hao Chi
- From the ‡Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS; University of Chinese Academy of Sciences; Institute of Computing Technology, CAS, Beijing 100190, China;.
| | - Ping Xu
- §State Key Laboratory of Proteomics; Beijing Proteome Research Center; National Center for Protein Sciences Beijing; Beijing Institute of Lifeomics, Beijing 102206, China;; ¶Key Laboratory of Combinatorial Biosynthesis and Drug Discovery of Ministry of Education Wuhan University, Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China;; College of Life Sciences, Hebei University, Baoding 071002, China.
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Hill LA, Vassiliadi DA, Dimopoulou I, Anderson AJ, Boyle LD, Kilgour AHM, Stimson RH, Machado Y, Overall CM, Walker BR, Lewis JG, Hammond GL. Neutrophil elastase-cleaved corticosteroid-binding globulin is absent in human plasma. J Endocrinol 2019; 240:27-39. [PMID: 30452386 PMCID: PMC6347282 DOI: 10.1530/joe-18-0479] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 09/28/2018] [Indexed: 12/24/2022]
Abstract
Corticosteroid-binding globulin (CBG) transports glucocorticoids in blood and is a serine protease inhibitor family member. Human CBG has a reactive center loop (RCL) which, when cleaved by neutrophil elastase (NE), disrupts its steroid-binding activity. Measurements of CBG levels are typically based on steroid-binding capacity or immunoassays. Discrepancies in ELISAs using monoclonal antibodies that discriminate between intact vs RCL-cleaved CBG have been interpreted as evidence that CBG with a cleaved RCL and low affinity for cortisol exists in the circulation. We examined the biochemical properties of plasma CBG in samples with discordant ELISA measurements and sought to identify RCL-cleaved CBG in human blood samples. Plasma CBG-binding capacity and ELISA values were consistent in arterial and venous blood draining skeletal muscle, liver and brain, as well as from a tissue (adipose) expected to contain activated neutrophils in obese individuals. Moreover, RCL-cleaved CBG was undetectable in plasma from critically ill patients, irrespective of whether their ELISA measurements were concordant or discordant. We found no evidence of RCL-cleaved CBG in plasma using a heat-dependent polymerization assay, and CBG that resists immunoprecipitation with a monoclonal antibody designed to specifically recognize an intact RCL, bound steroids with a high affinity. In addition, mass spectrometry confirmed the absence of NE-cleaved CBG in plasma in which ELISA values were highly discordant. Human CBG with a NE-cleaved RCL and low affinity for steroids is absent in blood samples, and CBG ELISA discrepancies likely reflect structural differences that alter epitopes recognized by specific monoclonal antibodies.
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Affiliation(s)
- Lesley A Hill
- Departments of Cellular and Physiological Sciences and Obstetrics and Gynaecology, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Dimitra A Vassiliadi
- Endocrine Unit, Second Department of Internal Medicine-Research Institute and Diabetes Center, Attiko University Hospital, Athens, Greece
| | - Ioanna Dimopoulou
- Endocrine Unit, Second Department of Internal Medicine-Research Institute and Diabetes Center, Attiko University Hospital, Athens, Greece
| | - Anna J Anderson
- BHF Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Luke D Boyle
- BHF Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Alixe H M Kilgour
- BHF Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Roland H Stimson
- BHF Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Yoan Machado
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Christopher M Overall
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Brian R Walker
- BHF Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - John G Lewis
- Canterbury Health Laboratories, Christchurch, New Zealand
| | - Geoffrey L Hammond
- Departments of Cellular and Physiological Sciences and Obstetrics and Gynaecology, The University of British Columbia, Vancouver, British Columbia, Canada
- Correspondence should be addressed to G L Hammond:
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Vinh NB, Drinkwater N, Malcolm TR, Kassiou M, Lucantoni L, Grin PM, Butler GS, Duffy S, Overall CM, Avery VM, Scammells PJ, McGowan S. Hydroxamic Acid Inhibitors Provide Cross-Species Inhibition of Plasmodium M1 and M17 Aminopeptidases. J Med Chem 2018; 62:622-640. [DOI: 10.1021/acs.jmedchem.8b01310] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Natalie B. Vinh
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Melbourne, VIC 3052, Australia
| | - Nyssa Drinkwater
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Melbourne, VIC 3800, Australia
| | - Tess R. Malcolm
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Melbourne, VIC 3800, Australia
| | - Michael Kassiou
- School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia
| | - Leonardo Lucantoni
- Discovery Biology, Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD 4111, Australia
| | | | | | - Sandra Duffy
- Discovery Biology, Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD 4111, Australia
| | | | - Vicky M. Avery
- Discovery Biology, Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD 4111, Australia
| | - Peter J. Scammells
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Melbourne, VIC 3052, Australia
| | - Sheena McGowan
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Melbourne, VIC 3800, Australia
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Omenn GS, Lane L, Overall CM, Corrales FJ, Schwenk JM, Paik YK, Van Eyk JE, Liu S, Snyder M, Baker MS, Deutsch EW. Progress on Identifying and Characterizing the Human Proteome: 2018 Metrics from the HUPO Human Proteome Project. J Proteome Res 2018; 17:4031-4041. [PMID: 30099871 PMCID: PMC6387656 DOI: 10.1021/acs.jproteome.8b00441] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [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: 02/07/2023]
Abstract
The Human Proteome Project (HPP) annually reports on progress throughout the field in credibly identifying and characterizing the human protein parts list and making proteomics an integral part of multiomics studies in medicine and the life sciences. NeXtProt release 2018-01-17, the baseline for this sixth annual HPP special issue of the Journal of Proteome Research, contains 17 470 PE1 proteins, 89% of all neXtProt predicted PE1-4 proteins, up from 17 008 in release 2017-01-23 and 13 975 in release 2012-02-24. Conversely, the number of neXtProt PE2,3,4 missing proteins has been reduced from 2949 to 2579 to 2186 over the past two years. Of the PE1 proteins, 16 092 are based on mass spectrometry results, and 1378 on other kinds of protein studies, notably protein-protein interaction findings. PeptideAtlas has 15 798 canonical proteins, up 625 over the past year, including 269 from SUMOylation studies. The largest reason for missing proteins is low abundance. Meanwhile, the Human Protein Atlas has released its Cell Atlas, Pathology Atlas, and updated Tissue Atlas, and is applying recommendations from the International Working Group on Antibody Validation. Finally, there is progress using the quantitative multiplex organ-specific popular proteins targeted proteomics approach in various disease categories.
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Affiliation(s)
- Gilbert S. Omenn
- Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, Michigan 48109-2218, United States
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109-5263, United States
| | - Lydie Lane
- CALIPHO Group, SIB Swiss Institute of Bioinformatics and Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, CMU, Michel-Servet 1, 1211 Geneva 4, Switzerland
| | - Christopher M. Overall
- Life Sciences Institute, Faculty of Dentistry, University of British Columbia, 2350 Health Sciences Mall, Room 4.401, Vancouver, BC Canada V6T 1Z3
| | | | - Jochen M. Schwenk
- Science for Life Laboratory, KTH Royal Institute of Technology, Tomtebodavägen 23A, 17165 Solna, Sweden
| | - Young-Ki Paik
- Yonsei Proteome Research Center, Room 425, Building #114, Yonsei University,50 Yonsei-ro, Seodaemoon-ku, Seoul 120-749, Korea
| | - Jennifer E. Van Eyk
- Advanced Clinical BioSystems Research Institute, Cedars Sinai Precision Biomarker Laboratories, Barbra Streisand Women’s Heart Center, Cedars-Sinai Medical Center, Los Angeles, CA 90048, United States
| | - Siqi Liu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, United States
| | - Michael Snyder
- Department of Genetics, Stanford University, Alway Building, 300 Pasteur Drive, 3165 Porter Drive, Palo Alto, 94304, United States
| | - Mark S. Baker
- Department of Biomedical Sciences, Macquarie University, NSW 2109, Australia
| | - Eric W. Deutsch
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109-5263, United States
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Paik YK, Lane L, Kawamura T, Chen YJ, Cho JY, LaBaer J, Yoo JS, Domont G, Corrales F, Omenn GS, Archakov A, Encarnación-Guevara S, Lui S, Salekdeh GH, Cho JY, Kim CY, Overall CM. Launching the C-HPP neXt-CP50 Pilot Project for Functional Characterization of Identified Proteins with No Known Function. J Proteome Res 2018; 17:4042-4050. [PMID: 30269496 PMCID: PMC6693327 DOI: 10.1021/acs.jproteome.8b00383] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [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: 12/18/2022]
Abstract
An important goal of the Human Proteome Organization (HUPO) Chromosome-centric Human Proteome Project (C-HPP) is to correctly define the number of canonical proteins encoded by their cognate open reading frames on each chromosome in the human genome. When identified with high confidence of protein evidence (PE), such proteins are termed PE1 proteins in the online database resource, neXtProt. However, proteins that have not been identified unequivocally at the protein level but that have other evidence suggestive of their existence (PE2-4) are termed missing proteins (MPs). The number of MPs has been reduced from 5511 in 2012 to 2186 in 2018 (neXtProt 2018-01-17 release). Although the annotation of the human proteome has made significant progress, the "parts list" alone does not inform function. Indeed, 1937 proteins representing ∼10% of the human proteome have no function either annotated from experimental characterization or predicted by homology to other proteins. Specifically, these 1937 "dark proteins" of the so-called dark proteome are composed of 1260 functionally uncharacterized but identified PE1 proteins, designated as uPE1, plus 677 MPs from categories PE2-PE4, which also have no known or predicted function and are termed uMPs. At the HUPO-2017 Annual Meeting, the C-HPP officially adopted the uPE1 pilot initiative, with 14 participating international teams later committing to demonstrate the feasibility of the functional characterization of large numbers of dark proteins (CP), starting first with 50 uPE1 proteins, in a stepwise chromosome-centric organizational manner. The second aim of the feasibility phase to characterize protein (CP) functions of 50 uPE1 proteins, termed the neXt-CP50 initiative, is to utilize a variety of approaches and workflows according to individual team expertise, interest, and resources so as to enable the C-HPP to recommend experimentally proven workflows to the proteome community within 3 years. The results from this pilot will not only be the cornerstone of a larger characterization initiative but also enhance understanding of the human proteome and integrated cellular networks for the discovery of new mechanisms of pathology, mechanistically informative biomarkers, and rational drug targets.
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Affiliation(s)
- Young-Ki Paik
- Yonsei Proteome Research Center and Department of Integrative Omics, Yonsei University, Sudaemoon-ku, Seoul, Korea
| | - Lydie Lane
- CALIPHO group, Swiss Institute of Bioinformatics & Department of Microbiology and Molecular medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Takeshi Kawamura
- Proteomics Laboratory, Isotope Science Center, The University of Tokyo, Bunkyo-Ku, Tokyo 113-0032 Japan
| | - Yu-Ju Chen
- Institute of Chemistry Academia Sinica, 128 Academia Road Sec. 2, Nankang Taipei 115 Taiwan
| | - Je-Yoel Cho
- Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul University, 1 Gwanak-, Gwanak-gu, 151-742 Seoul, South Korea
| | - Joshua LaBaer
- McAllister Ave. Arizona State University, Tempe, Arizona, 85287-5001, USA
| | - Jong Shin Yoo
- Division of Mass Spectrometry Research, Korea Basic Science Institute, Ochang, Korea
| | - Gilberto Domont
- Federal University of Rio de Janeiro Institute of Chemistry, Rio de Janeiro, RJ Brazil
| | - Fernando Corrales
- Functional Proteomics Laboratory National Center of Biotechnology, CSIC 28049 Madrid, Spain
| | - Gilbert S. Omenn
- Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109-2218, United States
| | | | | | - Siqi Lui
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
| | - Ghasem Hosseini Salekdeh
- Department of Molecular Systems Biology, Royan Institute for Stem Cell Biology and Technology, 1665659911, Tehran, Iran
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
| | - Jin-Young Cho
- Yonsei Proteome Research Center and Department of Integrative Omics, Yonsei University, Sudaemoon-ku, Seoul, Korea
| | - Chae-Yeon Kim
- Yonsei Proteome Research Center and Department of Integrative Omics, Yonsei University, Sudaemoon-ku, Seoul, Korea
| | - Christopher M. Overall
- Centre for Blood Research, Departments of Oral Biological & Medical Sciences, and Biochemistry & Molecular Biology, Faculty of Dentistry, University of British Columbia, Vancouver, Canada
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Affiliation(s)
- M Joanne Lemieux
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Jean-Bernard Denault
- Department of Pharmacology and Physiology, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Christopher M Overall
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3.,Department of Oral Biological and Medical Science, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3.,Center for Blood Research, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
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43
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Marshall NC, Klein T, Thejoe M, von Krosigk N, Kizhakkedathu J, Finlay BB, Overall CM. Global Profiling of Proteolysis from the Mitochondrial Amino Terminome during Early Intrinsic Apoptosis Prior to Caspase-3 Activation. J Proteome Res 2018; 17:4279-4296. [PMID: 30371095 DOI: 10.1021/acs.jproteome.8b00675] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [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: 02/07/2023]
Abstract
The human genome encodes ∼20 mitochondrial proteases, yet we know little of how they sculpt the mitochondrial proteome, particularly during important mitochondrial events such as the initiation of apoptosis. To characterize global mitochondrial proteolysis we refined our technique, terminal amine isotopic labeling of substrates, for mitochondrial SILAC (MS-TAILS) to identify proteolysis across mitochondria and parent cells in parallel. Our MS-TAILS analyses identified 45% of the mitochondrial proteome and identified protein amino (N)-termini from 26% of mitochondrial proteins, the highest reported coverage of the human mitochondrial N-terminome. MS-TAILS revealed 97 previously unknown proteolytic sites. MS-TAILS also identified mitochondrial targeting sequence (MTS) removal by proteolysis during protein import, confirming 101 MTS sites and identifying 135 new MTS sites, revealing a wobbly requirement for the MTS cleavage motif. To examine the relatively unknown initial cleavage events occurring before the well-studied activation of caspase-3 in intrinsic apoptosis, we quantitatively compared N-terminomes of mitochondria and their parent cells before and after initiation of apoptosis at very early time points. By identifying altered levels of >400 N-termini, MS-TAILS analyses implicated specific mitochondrial pathways including protein import, fission, and iron homeostasis in apoptosis initiation. Notably, both staurosporine and Bax activator molecule-7 triggered in common 7 mitochondrial and 85 cellular cleavage events that are potentially part of an essential core of apoptosis-initiating events. All mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium with the dataset identifier PXD009054.
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Affiliation(s)
- Natalie C Marshall
- Michael Smith Laboratories , University of British Columbia , Vancouver , British Columbia , V6T 1Z4 , Canada
| | | | - Maichael Thejoe
- Michael Smith Laboratories , University of British Columbia , Vancouver , British Columbia , V6T 1Z4 , Canada
| | - Niklas von Krosigk
- Michael Smith Laboratories , University of British Columbia , Vancouver , British Columbia , V6T 1Z4 , Canada
| | - Jayachandran Kizhakkedathu
- Department of Pathology and Laboratory Medicine and Department of Chemistry , University of British Columbia , Vancouver , British Columbia V6T 1Z2 , Canada
| | - B Brett Finlay
- Michael Smith Laboratories , University of British Columbia , Vancouver , British Columbia , V6T 1Z4 , Canada
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44
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Mallia-Milanes B, Dufour A, Philp C, Solis N, Klein T, Fischer M, Bolton CE, Shapiro S, Overall CM, Johnson SR. TAILS proteomics reveals dynamic changes in airway proteolysis controlling protease activity and innate immunity during COPD exacerbations. Am J Physiol Lung Cell Mol Physiol 2018; 315:L1003-L1014. [PMID: 30284925 DOI: 10.1152/ajplung.00175.2018] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [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: 01/05/2023] Open
Abstract
Dysregulated protease activity is thought to cause parenchymal and airway damage in chronic obstructive pulmonary disease (COPD). Multiple proteases have been implicated in COPD, and identifying their substrates may reveal new disease mechanisms and treatments. However, as proteases interact with many substrates that may be protease inhibitors or proteases themselves, these webs of protease interactions make the wider consequences of therapeutically targeting proteases difficult to predict. We therefore used a systems approach to determine protease substrates and protease activity in COPD airways. Protease substrates were determined by proteomics using the terminal amine isotopic labeling of substrates (TAILS) methodology in paired sputum samples during stable COPD and exacerbations. Protease activity and specific protein degradation in airway samples were assessed using Western blotting, substrate assays, and ex vivo cleavage assays. Two hundred ninety-nine proteins were identified in human COPD sputum, 125 of which were proteolytically processed, including proteases, protease inhibitors, mucins, defensins, and complement and other innate immune proteins. During exacerbations, airway neutrophils and neutrophil proteases increased and more proteins were cleaved, particularly at multiple sites, consistent with degradation and inactivation. During exacerbations, different substrates were processed, including protease inhibitors, mucins, and complement proteins. Exacerbations were associated with increasing airway elastase activity and increased processing of specific elastase substrates, including secretory leukocyte protease inhibitor. Proteolysis regulates multiple processes including elastase activity and innate immune proteins in COPD airways and differs during stable disease and exacerbations. The complexity of protease, inhibitor, and substrate networks makes the effect of protease inhibitors hard to predict which should be used cautiously.
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Affiliation(s)
- Brendan Mallia-Milanes
- Division of Respiratory Medicine and National Institute for Health Research Nottingham Biomedical Research Centre Respiratory Theme, University of Nottingham , Nottingham , United Kingdom
| | - Antoine Dufour
- Departments of Oral Biological and Medical Sciences, Biochemistry and Molecular Biology and Centre for Blood Research, Life Sciences Institute, Faculty of Dentistry, University of British Columbia , Vancouver, British Columbia , Canada
| | - Christopher Philp
- Division of Respiratory Medicine and National Institute for Health Research Nottingham Biomedical Research Centre Respiratory Theme, University of Nottingham , Nottingham , United Kingdom.,Nottingham Molecular Pathology Node, University of Nottingham , Nottingham , United Kingdom
| | - Nestor Solis
- Departments of Oral Biological and Medical Sciences, Biochemistry and Molecular Biology and Centre for Blood Research, Life Sciences Institute, Faculty of Dentistry, University of British Columbia , Vancouver, British Columbia , Canada
| | - Theo Klein
- Departments of Oral Biological and Medical Sciences, Biochemistry and Molecular Biology and Centre for Blood Research, Life Sciences Institute, Faculty of Dentistry, University of British Columbia , Vancouver, British Columbia , Canada
| | - Marlies Fischer
- Division of Respiratory Medicine and National Institute for Health Research Nottingham Biomedical Research Centre Respiratory Theme, University of Nottingham , Nottingham , United Kingdom.,Nottingham Molecular Pathology Node, University of Nottingham , Nottingham , United Kingdom
| | - Charlotte E Bolton
- Division of Respiratory Medicine and National Institute for Health Research Nottingham Biomedical Research Centre Respiratory Theme, University of Nottingham , Nottingham , United Kingdom
| | - Steven Shapiro
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh , Pittsburgh, Pennsylvania
| | - Christopher M Overall
- Departments of Oral Biological and Medical Sciences, Biochemistry and Molecular Biology and Centre for Blood Research, Life Sciences Institute, Faculty of Dentistry, University of British Columbia , Vancouver, British Columbia , Canada
| | - Simon R Johnson
- Division of Respiratory Medicine and National Institute for Health Research Nottingham Biomedical Research Centre Respiratory Theme, University of Nottingham , Nottingham , United Kingdom.,Nottingham Molecular Pathology Node, University of Nottingham , Nottingham , United Kingdom
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45
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Abstract
This special issue of JPR celebrates the fifth anniversary of the Chromosome-Centric Human Proteome Project (C-HPP). We present 27 manuscripts in four categories: (i) Metrics of Progress and Resources, (ii) Missing Protein Detection and Validation, (iii) Analytical Methods and Quality Assessment, and (iv) Protein Functions and Disease. We briefly introduce key messages from each paper, mostly from C-HPP teams and some from the Biology and Disease-driven HPP. From the first few months of the C-HPP NeXt-MP50 Missing Proteins Challenge, authors report 73 missing protein detections that meet the HPP guidelines using several novel approaches. Finally, we discuss future directions.
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Affiliation(s)
- Young-Ki Paik
- Yonsei Proteome Research Center and Department of Biochemistry, Yonsei University
| | - Christopher M Overall
- Centre for Blood Research, Departments of Oral Biological & Medical Sciences and Biochemistry & Molecular Biology, Faculty of Dentistry, University of British Columbia
| | | | - Jennifer E Van Eyk
- Advanced Clinical BioSystems Research Institute , Department of Medicine, Cedars-Sinai Medical Centre
| | - Gilbert S Omenn
- Institute for Systems Biology.,Departments of Computational Medicine & Bioinformatics, Internal Medicine, and Human Genetics and School of Public Health, University of Michigan
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46
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Folgueras AR, Fueyo A, García-Suárez O, Cox J, Astudillo A, Tortorella P, Campestre C, Gutiérrez-Fernández A, Fanjul-Fernández M, Pennington CJ, Edwards DR, Overall CM, López-Otín C. Collagenase-2 deficiency or inhibition impairs experimental autoimmune encephalomyelitis in mice. J Biol Chem 2018; 293:11968-11969. [DOI: 10.1074/jbc.aac118.004703] [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: 11/06/2022] Open
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47
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Russo V, Klein T, Lim DJ, Solis N, Machado Y, Hiroyasu S, Nabai L, Shen Y, Zeglinski MR, Zhao H, Oram CP, Lennox PA, Van Laeken N, Carr NJ, Crawford RI, Franzke CW, Overall CM, Granville DJ. Granzyme B is elevated in autoimmune blistering diseases and cleaves key anchoring proteins of the dermal-epidermal junction. Sci Rep 2018; 8:9690. [PMID: 29946113 PMCID: PMC6018769 DOI: 10.1038/s41598-018-28070-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [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: 01/12/2018] [Accepted: 06/15/2018] [Indexed: 01/23/2023] Open
Abstract
In healthy skin, epidermis and dermis are anchored together at the dermal-epidermal junction (DEJ), a specialized basement membrane pivotal for skin integrity and function. However, increased inflammation in the DEJ is associated with the disruption and separation of this junction and sub-epidermal blistering. Granzyme B (GzmB) is a serine protease secreted by immune cells. Dysregulated inflammation may lead to increased GzmB accumulation and proteolysis in the extracellular milieu. Although elevated GzmB is observed at the level of the DEJ in inflammatory and blistering skin conditions, the present study is the first to explore GzmB in the context of DEJ degradation in autoimmune sub-epidermal blistering. In the present study, GzmB induced separation of the DEJ in healthy human skin. Subsequently, α6/β4 integrin, collagen VII, and collagen XVII were identified as extracellular substrates for GzmB through western blot, and specific cleavage sites were identified by mass spectrometry. In human bullous pemphigoid, dermatitis herpetiformis, and epidermolysis bullosa acquisita, GzmB was elevated at the DEJ when compared to healthy samples, while α6/β4 integrin, collagen VII, and collagen XVII were reduced or absent in the area of blistering. In summary, our results suggest that regardless of the initial causation of sub-epidermal blistering, GzmB activity is a common final pathway that could be amenable to a single targeted treatment approach.
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Affiliation(s)
- Valerio Russo
- International Collaboration On Repair Discoveries (ICORD) Research Centre, Vancouver, BC, V5Z 1M9, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
- BC Professional Firefighters' Burn and Wound Healing Research Laboratory, Vancouver, BC, V5Z 1M9, Canada
| | - Theo Klein
- Centre for Blood Research, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
- Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Darielle J Lim
- International Collaboration On Repair Discoveries (ICORD) Research Centre, Vancouver, BC, V5Z 1M9, Canada
| | - Nestor Solis
- Centre for Blood Research, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
- Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Yoan Machado
- Centre for Blood Research, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
- Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Sho Hiroyasu
- International Collaboration On Repair Discoveries (ICORD) Research Centre, Vancouver, BC, V5Z 1M9, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
- BC Professional Firefighters' Burn and Wound Healing Research Laboratory, Vancouver, BC, V5Z 1M9, Canada
| | - Layla Nabai
- International Collaboration On Repair Discoveries (ICORD) Research Centre, Vancouver, BC, V5Z 1M9, Canada
- BC Professional Firefighters' Burn and Wound Healing Research Laboratory, Vancouver, BC, V5Z 1M9, Canada
| | - Yue Shen
- International Collaboration On Repair Discoveries (ICORD) Research Centre, Vancouver, BC, V5Z 1M9, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
- BC Professional Firefighters' Burn and Wound Healing Research Laboratory, Vancouver, BC, V5Z 1M9, Canada
| | - Matthew R Zeglinski
- International Collaboration On Repair Discoveries (ICORD) Research Centre, Vancouver, BC, V5Z 1M9, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
- BC Professional Firefighters' Burn and Wound Healing Research Laboratory, Vancouver, BC, V5Z 1M9, Canada
| | - Hongyan Zhao
- International Collaboration On Repair Discoveries (ICORD) Research Centre, Vancouver, BC, V5Z 1M9, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
- BC Professional Firefighters' Burn and Wound Healing Research Laboratory, Vancouver, BC, V5Z 1M9, Canada
| | - Cameron P Oram
- International Collaboration On Repair Discoveries (ICORD) Research Centre, Vancouver, BC, V5Z 1M9, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
- BC Professional Firefighters' Burn and Wound Healing Research Laboratory, Vancouver, BC, V5Z 1M9, Canada
| | - Peter A Lennox
- Department of Surgery, University of British Columbia, Vancouver, BC, V5Z 1M9, Canada
| | - Nancy Van Laeken
- Department of Surgery, University of British Columbia, Vancouver, BC, V5Z 1M9, Canada
| | - Nick J Carr
- Department of Surgery, University of British Columbia, Vancouver, BC, V5Z 1M9, Canada
| | - Richard I Crawford
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
- Department of Dermatology and Skin Science, University of British Columbia, Vancouver, BC, V5Z 4E8, Canada
| | - Claus-Werner Franzke
- Department of Dermatology, Medical Center and Faculty of Medicine - University of Freiburg, 79104, Freiburg, Germany
| | - Christopher M Overall
- Centre for Blood Research, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
- Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - David J Granville
- International Collaboration On Repair Discoveries (ICORD) Research Centre, Vancouver, BC, V5Z 1M9, Canada.
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada.
- BC Professional Firefighters' Burn and Wound Healing Research Laboratory, Vancouver, BC, V5Z 1M9, Canada.
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48
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Dufour A, Bellac CL, Eckhard U, Solis N, Klein T, Kappelhoff R, Fortelny N, Jobin P, Rozmus J, Mark J, Pavlidis P, Dive V, Barbour SJ, Overall CM. C-terminal truncation of IFN-γ inhibits proinflammatory macrophage responses and is deficient in autoimmune disease. Nat Commun 2018; 9:2416. [PMID: 29925830 PMCID: PMC6010466 DOI: 10.1038/s41467-018-04717-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [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: 04/08/2017] [Accepted: 05/18/2018] [Indexed: 01/02/2023] Open
Abstract
Controlled macrophage differentiation and activation in the initiation and resolution of inflammation is crucial for averting progression to chronic inflammatory and autoimmune diseases. Here we show a negative feedback mechanism for proinflammatory IFN-γ activation of macrophages driven by macrophage-associated matrix metalloproteinase 12 (MMP12). Through C-terminal truncation of IFN-γ at 135Glu↓Leu136 the IFN-γ receptor-binding site was efficiently removed thereby reducing JAK-STAT1 signaling and IFN-γ activation of proinflammatory macrophages. In acute peritonitis this signature was absent in Mmp12–/– mice and recapitulated in Mmp12+/+ mice treated with a MMP12-specific inhibitor. Similarly, loss-of-MMP12 increases IFN-γ–dependent proinflammatory markers and iNOS+/MHC class II+ macrophage accumulation with worse lymphadenopathy, arthritic synovitis and lupus glomerulonephritis. In active human systemic lupus erythematosus, MMP12 levels were lower and IFN-γ higher compared to treated patients or healthy individuals. Hence, macrophage proteolytic truncation of IFN-γ attenuates classical activation of macrophages as a prelude for resolving inflammation. IFN-γ is central in inflammatory pathogenesis, response to infection and autoimmune diseases. Here the authors show that MMP12 expression is reduced in patients with SLE and that MMP12 post-translationally truncates IFN-y, inhibiting its function and affecting pathogenesis of mouse models of peritonitis, SLE and rheumatoid arthritis.
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Affiliation(s)
- Antoine Dufour
- Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, 4.401-2350 Health Sciences Mall, Vancouver, V6T 1Z3, BC, Canada.,Centre for Blood Research, 4.401-2350 Health Sciences Mall, Vancouver, V6T 1Z3, BC, Canada.,Department of Physiology and Pharmacology McCaig Institute for Bone and Joint Health, Cumming School of Medicine, HRIC 3C64 3330 Hospital, Dr NW Calgary, T2N 4N1, AB, Canada
| | - Caroline L Bellac
- Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, 4.401-2350 Health Sciences Mall, Vancouver, V6T 1Z3, BC, Canada.,Centre for Blood Research, 4.401-2350 Health Sciences Mall, Vancouver, V6T 1Z3, BC, Canada.,Swissmedic, Swiss Agency for Therapeutics Products, Hallerstrasse 7, P.O. Box, Bern 9, CH-3000, Switzerland
| | - Ulrich Eckhard
- Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, 4.401-2350 Health Sciences Mall, Vancouver, V6T 1Z3, BC, Canada.,Centre for Blood Research, 4.401-2350 Health Sciences Mall, Vancouver, V6T 1Z3, BC, Canada
| | - Nestor Solis
- Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, 4.401-2350 Health Sciences Mall, Vancouver, V6T 1Z3, BC, Canada.,Centre for Blood Research, 4.401-2350 Health Sciences Mall, Vancouver, V6T 1Z3, BC, Canada
| | - Theo Klein
- Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, 4.401-2350 Health Sciences Mall, Vancouver, V6T 1Z3, BC, Canada.,Centre for Blood Research, 4.401-2350 Health Sciences Mall, Vancouver, V6T 1Z3, BC, Canada
| | - Reinhild Kappelhoff
- Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, 4.401-2350 Health Sciences Mall, Vancouver, V6T 1Z3, BC, Canada.,Centre for Blood Research, 4.401-2350 Health Sciences Mall, Vancouver, V6T 1Z3, BC, Canada
| | - Nikolaus Fortelny
- Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, 4.401-2350 Health Sciences Mall, Vancouver, V6T 1Z3, BC, Canada.,Centre for Blood Research, 4.401-2350 Health Sciences Mall, Vancouver, V6T 1Z3, BC, Canada.,Department of Biochemistry and Molecular Biology, University of British Columbia, 4.401-2350 Health Sciences Mall, Vancouver, V6T 1Z3, BC, Canada
| | - Parker Jobin
- Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, 4.401-2350 Health Sciences Mall, Vancouver, V6T 1Z3, BC, Canada.,Centre for Blood Research, 4.401-2350 Health Sciences Mall, Vancouver, V6T 1Z3, BC, Canada.,Department of Biochemistry and Molecular Biology, University of British Columbia, 4.401-2350 Health Sciences Mall, Vancouver, V6T 1Z3, BC, Canada
| | - Jacob Rozmus
- Department of Pediatrics, Child and Family Research Institute and BC Children's Hospital, University of British Columbia, 3110A-950 West 28th Av, Vancouver, V5Z 4H4, BC, Canada
| | - Jennifer Mark
- Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, 4.401-2350 Health Sciences Mall, Vancouver, V6T 1Z3, BC, Canada.,Centre for Blood Research, 4.401-2350 Health Sciences Mall, Vancouver, V6T 1Z3, BC, Canada
| | - Paul Pavlidis
- Centre for High Throughput Biology, University of British Columbia, 2125 East Mall, Vancouver, V6T 1Z3, BC, Canada.,Department of Psychiatry, University of British Columbia, 2125 East Mall, Vancouver, V6T 1Z3, BC, Canada
| | - Vincent Dive
- Commissariat a l'Energie Atomique (CEA) CE-Saclay, Labex LERMIT, Service d'Ingenierie Moleculaire des Proteines, Bat 152, Gif/Yvette, 91191, France
| | - Sean J Barbour
- Department of Medicine, University of British Columbia, 2775 Laurel St, Vancouver, V6T 1Z3, BC, Canada
| | - Christopher M Overall
- Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, 4.401-2350 Health Sciences Mall, Vancouver, V6T 1Z3, BC, Canada. .,Centre for Blood Research, 4.401-2350 Health Sciences Mall, Vancouver, V6T 1Z3, BC, Canada. .,Department of Biochemistry and Molecular Biology, University of British Columbia, 4.401-2350 Health Sciences Mall, Vancouver, V6T 1Z3, BC, Canada.
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49
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Tharmarajah G, Eckhard U, Jain F, Marino G, Prudova A, Urtatiz O, Fuchs H, de Angelis MH, Overall CM, Van Raamsdonk CD. Melanocyte development in the mouse tail epidermis requires the Adamts9 metalloproteinase. Pigment Cell Melanoma Res 2018; 31:693-707. [PMID: 29781574 DOI: 10.1111/pcmr.12711] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 04/17/2018] [Accepted: 04/24/2018] [Indexed: 12/13/2022]
Abstract
The mouse tail has an important role in the study of melanogenesis, because mouse tail skin can be used to model human skin pigmentation. To better understand the development of melanocytes in the mouse tail, we cloned two dominant ENU-generated mutations of the Adamts9 gene, Und3 and Und4, which cause an unpigmented ring of epidermis in the middle of the tail, but do not alter pigmentation in the rest of the mouse. Adamts9 encodes a widely expressed zinc metalloprotease with thrombospondin type 1 repeats with few known substrates. Melanocytes are lost in the Adamts9 mutant tail epidermis at a relatively late stage of development, around E18.5. Studies of our Adamts9 conditional allele suggest that there is a melanocyte cell-autonomous requirement for Adamts9. In addition, we used a proteomics approach, TAILS N-terminomics, to identify new Adamts9 candidate substrates in the extracellular matrix of the skin. The tail phenotype of Adamts9 mutants is strikingly similar to the unpigmented trunk belt in Adamts20 mutants, which suggests a particular requirement for Adamts family activity at certain positions along the anterior-posterior axis.
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Affiliation(s)
- Grace Tharmarajah
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - Ulrich Eckhard
- Department of Oral Biological and Medical Sciences, Faculty of Dentistry, Centre for Blood Research, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - Fagun Jain
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - Giada Marino
- Department of Oral Biological and Medical Sciences, Faculty of Dentistry, Centre for Blood Research, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - Anna Prudova
- Department of Oral Biological and Medical Sciences, Faculty of Dentistry, Centre for Blood Research, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - Oscar Urtatiz
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - Helmut Fuchs
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum Munchen, German Research Centre for Environmental Health, Neuherberg, Germany
| | - Martin H de Angelis
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum Munchen, German Research Centre for Environmental Health, Neuherberg, Germany.,Chair of Experimental Genetics, School of Life Science, Weihenstephan Technische Universitat, Freising, Germany.,German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Christopher M Overall
- Department of Oral Biological and Medical Sciences, Faculty of Dentistry, Centre for Blood Research, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada.,Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - Catherine D Van Raamsdonk
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
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50
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King SL, Goth CK, Eckhard U, Joshi HJ, Haue AD, Vakhrushev SY, Schjoldager KT, Overall CM, Wandall HH. TAILS N-terminomics and proteomics reveal complex regulation of proteolytic cleavage by O-glycosylation. J Biol Chem 2018; 293:7629-7644. [PMID: 29593093 PMCID: PMC5961060 DOI: 10.1074/jbc.ra118.001978] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 03/27/2018] [Indexed: 12/31/2022] Open
Abstract
Proteolytic processing is an irreversible post-translational modification functioning as a ubiquitous regulator of cellular activity. Protease activity is tightly regulated via control of gene expression, enzyme and substrate compartmentalization, zymogen activation, enzyme inactivation, and substrate availability. Emerging evidence suggests that proteolysis can also be regulated by substrate glycosylation and that glycosylation of individual sites on a substrate can decrease or, in rare cases, increase its sensitivity to proteolysis. Here, we investigated the relationship between site-specific, mucin-type (or GalNAc-type) O-glycosylation and proteolytic cleavage of extracellular proteins. Using in silico analysis, we found that O-glycosylation and cleavage sites are significantly associated with each other. We then used a positional proteomic strategy, terminal amine isotopic labeling of substrates (TAILS), to map the in vivo cleavage sites in HepG2 SimpleCells with and without one of the key initiating GalNAc transferases, GalNAc-T2, and after treatment with exogenous matrix metalloproteinase 9 (MMP9) or neutrophil elastase. Surprisingly, we found that loss of GalNAc-T2 not only increased cleavage, but also decreased cleavage across a broad range of other substrates, including key regulators of the protease network. We also found altered processing of several central regulators of lipid homeostasis, including apolipoprotein B and the phospholipid transfer protein, providing new clues to the previously reported link between GALNT2 and lipid homeostasis. In summary, we show that loss of GalNAc-T2 O-glycosylation leads to a general decrease in cleavage and that GalNAc-T2 O-glycosylation affects key regulators of the cellular proteolytic network, including multiple members of the serpin family.
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Affiliation(s)
- Sarah L King
- From the Department of Cellular and Molecular Medicine, Centre for Glycomics, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark and
| | - Christoffer K Goth
- From the Department of Cellular and Molecular Medicine, Centre for Glycomics, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark and
| | - Ulrich Eckhard
- the Centre for Blood Research, Department of Oral Biological and Medical Sciences, Faculty of Dentistry, and Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Hiren J Joshi
- From the Department of Cellular and Molecular Medicine, Centre for Glycomics, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark and
| | - Amalie D Haue
- From the Department of Cellular and Molecular Medicine, Centre for Glycomics, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark and
| | - Sergey Y Vakhrushev
- From the Department of Cellular and Molecular Medicine, Centre for Glycomics, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark and
| | - Katrine T Schjoldager
- From the Department of Cellular and Molecular Medicine, Centre for Glycomics, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark and
| | - Christopher M Overall
- the Centre for Blood Research, Department of Oral Biological and Medical Sciences, Faculty of Dentistry, and Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Hans H Wandall
- From the Department of Cellular and Molecular Medicine, Centre for Glycomics, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark and
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