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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] [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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Rhys HI, Dell'Accio F, Pitzalis C, Moore A, Norling LV, Perretti M. Neutrophil Microvesicles from Healthy Control and Rheumatoid Arthritis Patients Prevent the Inflammatory Activation of Macrophages. EBioMedicine 2018; 29:60-69. [PMID: 29449195 PMCID: PMC5925578 DOI: 10.1016/j.ebiom.2018.02.003] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 01/24/2018] [Accepted: 02/01/2018] [Indexed: 12/11/2022] Open
Abstract
Microvesicles (MVs) are emerging as a novel means to enact cell-to-cell communication in inflammation. Here, we aimed to ascertain the ability of neutrophil-derived MVs to modulate target cell behaviour, the focus being the macrophage. MVs were generated in response to tumour necrosis factor-α, from healthy control neutrophils or those from rheumatoid arthritis patients. MVs were used to stimulate human monocyte-derived macrophages in vitro, or administered intra-articularly in the K/BxN mouse model of arthritis. A macrophage/fibroblast-like synoviocyte co-culture system was used to study the effects of vesicles on the crosstalk between these cells. We demonstrate a direct role for phosphatidylserine and annexin-A1 exposed by the MVs to counteract classical activation of the macrophages, and promote the release of transforming growth factor-β, respectively. Classically-activated macrophages exposed to neutrophil MVs no longer activated fibroblast-like synoviocytes in subsequent co-culture settings. Finally, intra-articular administration of neutrophil MVs from rheumatoid arthritis patients in arthritic mice affected the phenotype of joint macrophages. Altogether these data, with the identification of specific MV determinants, open new opportunities to modulate on-going inflammation in the synovia - mainly by affecting macrophage polarization and potentially also fibroblast-like synoviocytes - through the delivery of autologous or heterologous MVs produced from neutrophils.
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Affiliation(s)
- Hefin I Rhys
- The William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, United Kingdom
| | - Francesco Dell'Accio
- The William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, United Kingdom; Centre for inflammation and therapeutic innovation, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, United Kingdom
| | - Costantino Pitzalis
- The William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, United Kingdom; Centre for inflammation and therapeutic innovation, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, United Kingdom
| | - Adrian Moore
- Centre for inflammation and therapeutic innovation, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, United Kingdom; UCB Pharma, Bath Road, Slough, United Kingdom
| | - Lucy V Norling
- The William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, United Kingdom; Centre for inflammation and therapeutic innovation, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, United Kingdom.
| | - Mauro Perretti
- The William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, United Kingdom; Centre for inflammation and therapeutic innovation, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, United Kingdom.
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53
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Halstead ES, Umstead TM, Davies ML, Kawasawa YI, Silveyra P, Howyrlak J, Yang L, Guo W, Hu S, Hewage EK, Chroneos ZC. GM-CSF overexpression after influenza a virus infection prevents mortality and moderates M1-like airway monocyte/macrophage polarization. Respir Res 2018; 19:3. [PMID: 29304863 PMCID: PMC5756339 DOI: 10.1186/s12931-017-0708-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 12/18/2017] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Influenza A viruses cause life-threatening pneumonia and lung injury in the lower respiratory tract. Application of high GM-CSF levels prior to infection has been shown to reduce morbidity and mortality from pathogenic influenza infection in mice, but the mechanisms of protection and treatment efficacy have not been established. METHODS Mice were infected intranasally with influenza A virus (PR8 strain). Supra-physiologic levels of GM-CSF were induced in the airways using the double transgenic GM-CSF (DTGM) or littermate control mice starting on 3 days post-infection (dpi). Assessment of respiratory mechanical parameters was performed using the flexiVent rodent ventilator. RNA sequence analysis was performed on FACS-sorted airway macrophage subsets at 8 dpi. RESULTS Supra-physiologic levels of GM-CSF conferred a survival benefit, arrested the deterioration of lung mechanics, and reduced the abundance of protein exudates in bronchoalveolar (BAL) fluid to near baseline levels. Transcriptome analysis, and subsequent validation ELISA assays, revealed that excess GM-CSF re-directs macrophages from an "M1-like" to a more "M2-like" activation state as revealed by alterations in the ratios of CXCL9 and CCL17 in BAL fluid, respectively. Ingenuity pathway analysis predicted that GM-CSF surplus during IAV infection elicits expression of anti-inflammatory mediators and moderates M1 macrophage pro-inflammatory signaling by Type II interferon (IFN-γ). CONCLUSIONS Our data indicate that application of high levels of GM-CSF in the lung after influenza A virus infection alters pathogenic "M1-like" macrophage inflammation. These results indicate a possible therapeutic strategy for respiratory virus-associated pneumonia and acute lung injury.
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Affiliation(s)
- E. Scott Halstead
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA USA
- Pulmonary Immunology and Physiology Laboratory, Pennsylvania State University College of Medicine, Hershey, PA USA
| | - Todd M. Umstead
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA USA
- Pulmonary Immunology and Physiology Laboratory, Pennsylvania State University College of Medicine, Hershey, PA USA
| | - Michael L. Davies
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA USA
- Pulmonary Immunology and Physiology Laboratory, Pennsylvania State University College of Medicine, Hershey, PA USA
| | - Yuka Imamura Kawasawa
- Departments of Pharmacology & Biochemistry and Molecular Biology, Institute for Personalized Medicine, Pennsylvania State University College of Medicine, Hershey, PA USA
| | - Patricia Silveyra
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA USA
- Pulmonary Immunology and Physiology Laboratory, Pennsylvania State University College of Medicine, Hershey, PA USA
| | - Judie Howyrlak
- Departments of Medicine and Public Health Sciences, Pennsylvania State University College of Medicine, Hershey, PA USA
| | - Linlin Yang
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA USA
- Pulmonary Immunology and Physiology Laboratory, Pennsylvania State University College of Medicine, Hershey, PA USA
| | - Weichao Guo
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA USA
- Pulmonary Immunology and Physiology Laboratory, Pennsylvania State University College of Medicine, Hershey, PA USA
| | - Sanmei Hu
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA USA
- Pulmonary Immunology and Physiology Laboratory, Pennsylvania State University College of Medicine, Hershey, PA USA
| | - Eranda Kurundu Hewage
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA USA
- Pulmonary Immunology and Physiology Laboratory, Pennsylvania State University College of Medicine, Hershey, PA USA
| | - Zissis C. Chroneos
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA USA
- Pulmonary Immunology and Physiology Laboratory, Pennsylvania State University College of Medicine, Hershey, PA USA
- Department of Microbiology and Immunology, Pennsylvania State University College of Medicine, Hershey, PA USA
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Klein T, Eckhard U, Dufour A, Solis N, Overall CM. Proteolytic Cleavage-Mechanisms, Function, and "Omic" Approaches for a Near-Ubiquitous Posttranslational Modification. Chem Rev 2017; 118:1137-1168. [PMID: 29265812 DOI: 10.1021/acs.chemrev.7b00120] [Citation(s) in RCA: 123] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Proteases enzymatically hydrolyze peptide bonds in substrate proteins, resulting in a widespread, irreversible posttranslational modification of the protein's structure and biological function. Often regarded as a mere degradative mechanism in destruction of proteins or turnover in maintaining physiological homeostasis, recent research in the field of degradomics has led to the recognition of two main yet unexpected concepts. First, that targeted, limited proteolytic cleavage events by a wide repertoire of proteases are pivotal regulators of most, if not all, physiological and pathological processes. Second, an unexpected in vivo abundance of stable cleaved proteins revealed pervasive, functionally relevant protein processing in normal and diseased tissue-from 40 to 70% of proteins also occur in vivo as distinct stable proteoforms with undocumented N- or C-termini, meaning these proteoforms are stable functional cleavage products, most with unknown functional implications. In this Review, we discuss the structural biology aspects and mechanisms of catalysis by different protease classes. We also provide an overview of biological pathways that utilize specific proteolytic cleavage as a precision control mechanism in protein quality control, stability, localization, and maturation, as well as proteolytic cleavage as a mediator in signaling pathways. Lastly, we provide a comprehensive overview of analytical methods and approaches to study activity and substrates of proteolytic enzymes in relevant biological models, both historical and focusing on state of the art proteomics techniques in the field of degradomics research.
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Affiliation(s)
- Theo Klein
- Life Sciences Institute, Department of Oral Biological and Medical Sciences, and ‡Department of Biochemistry and Molecular Biology, University of British Columbia , Vancouver, British Columbia V6T 1Z4, Canada
| | - Ulrich Eckhard
- Life Sciences Institute, Department of Oral Biological and Medical Sciences, and ‡Department of Biochemistry and Molecular Biology, University of British Columbia , Vancouver, British Columbia V6T 1Z4, Canada
| | - Antoine Dufour
- Life Sciences Institute, Department of Oral Biological and Medical Sciences, and ‡Department of Biochemistry and Molecular Biology, University of British Columbia , Vancouver, British Columbia V6T 1Z4, Canada
| | - Nestor Solis
- Life Sciences Institute, Department of Oral Biological and Medical Sciences, and ‡Department of Biochemistry and Molecular Biology, University of British Columbia , Vancouver, British Columbia V6T 1Z4, Canada
| | - Christopher M Overall
- Life Sciences Institute, Department of Oral Biological and Medical Sciences, and ‡Department of Biochemistry and Molecular Biology, University of British Columbia , Vancouver, British Columbia V6T 1Z4, Canada
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55
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Ceeraz S, Eszterhas SK, Sergent PA, Armstrong DA, Ashare A, Broughton T, Wang L, Pechenick D, Burns CM, Noelle RJ, Vincenti MP, Fava RA. VISTA deficiency attenuates antibody-induced arthritis and alters macrophage gene expression in response to simulated immune complexes. Arthritis Res Ther 2017; 19:270. [PMID: 29216931 PMCID: PMC5721690 DOI: 10.1186/s13075-017-1474-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 11/14/2017] [Indexed: 12/17/2022] Open
Abstract
Background In addition to activated T cells, the immune checkpoint inhibitor “V domain-containing Ig suppressor of T-cell activation” (VISTA) is expressed by myeloid cell types, including macrophages and neutrophils. The importance of VISTA expression by myeloid cells to antibody-induced arthritis and its potential for relevance in human disease was evaluated. Methods VISTA was immunolocalized in normal and arthritic human synovial tissue sections and synovial tissue lysates were subjected to western blot analysis. The collagen antibody-induced arthritis model (CAIA) was performed with DBA/1 J mice treated with antibodies against VISTA and with VISTA-deficient mice (V-KO). Total mRNA from arthritic joints, spleens, and cultured macrophages was analyzed with NanoString arrays. Cytokines secreted by splenic inflammatory macrophages were determined. In-vitro chemotaxis and signal transduction assays were performed with cultured macrophages. Results VISTA protein was localized to synovial membrane cells, neutrophils, and scattered cells in lymphocyte-rich foci and was detected by western blot analysis in normal synovium and synovium from rheumatoid arthritis patients. Deficiency of VISTA or treatment of mice with anti-VISTA monoclonal antibodies attenuated CAIA. Joint damage and MMP-3 expression were significantly reduced in V-KO mice. Surface expression of C5a receptor was reduced on monocytes, neutrophils, and cultured macrophages from V-KO. Upon Fc receptor engagement in vitro, gene expression by V-KO macrophages was altered profoundly compared to WT, including a significant induction of IL-1 receptor antagonist (IL1rn). Conclusions VISTA expression supports immune-complex inflammation in CAIA and VISTA is expressed in human synovium. VISTA supports optimal responses to C5a and modulates macrophage responses to immune complexes. Electronic supplementary material The online version of this article (doi:10.1186/s13075-017-1474-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sabrina Ceeraz
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Lebanon, NH, 03756, USA.,Norris Cotton Cancer Center, Dartmouth Hitchcock Medical Center, Lebanon, NH, 03756, USA
| | - Susan K Eszterhas
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Lebanon, NH, 03756, USA.,Department of Veterans Affairs, Research Service, White River Junction, VT, 05009, USA
| | - Petra A Sergent
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Lebanon, NH, 03756, USA.,Norris Cotton Cancer Center, Dartmouth Hitchcock Medical Center, Lebanon, NH, 03756, USA
| | - David A Armstrong
- Pulmonary and Critical Care Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA.,Department of Medicine, Geisel School of Medicine at Dartmouth, Dartmouth Hitchcock Medical Center, Lebanon, NH, 03756, USA
| | - Alix Ashare
- Pulmonary and Critical Care Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA.,Department of Medicine, Geisel School of Medicine at Dartmouth, Dartmouth Hitchcock Medical Center, Lebanon, NH, 03756, USA
| | - Thomas Broughton
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Lebanon, NH, 03756, USA.,Norris Cotton Cancer Center, Dartmouth Hitchcock Medical Center, Lebanon, NH, 03756, USA
| | - Li Wang
- Microbiology and Immunology & Cancer Center Medical College of Wisconsin, Milwaukee, WI, USA
| | - Dov Pechenick
- ImmuNext INC, 1 Medical Center Drive, Lebanon, NH, 03756, USA
| | - Christopher M Burns
- Department of Medicine, Section of Rheumatology, Geisel School of Medicine at Dartmouth, Dartmouth-Hitchcock Medical Center, 1 Medical Center Drive, Lebanon, NH, 03756, USA
| | - Randolph J Noelle
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Lebanon, NH, 03756, USA.,Norris Cotton Cancer Center, Dartmouth Hitchcock Medical Center, Lebanon, NH, 03756, USA.,ImmuNext INC, 1 Medical Center Drive, Lebanon, NH, 03756, USA
| | - Matthew P Vincenti
- Department of Veterans Affairs, Research Service, White River Junction, VT, 05009, USA.,Department of Medicine, Geisel School of Medicine at Dartmouth, Dartmouth Hitchcock Medical Center, Lebanon, NH, 03756, USA
| | - Roy A Fava
- Department of Veterans Affairs, Research Service, White River Junction, VT, 05009, USA. .,Department of Medicine, Geisel School of Medicine at Dartmouth, Dartmouth Hitchcock Medical Center, Lebanon, NH, 03756, USA.
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56
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Matrix metalloproteinases as regulators of inflammatory processes. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2017; 1864:2036-2042. [DOI: 10.1016/j.bbamcr.2017.05.010] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 05/06/2017] [Accepted: 05/09/2017] [Indexed: 12/26/2022]
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57
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Amar S, Minond D, Fields GB. Clinical Implications of Compounds Designed to Inhibit ECM-Modifying Metalloproteinases. Proteomics 2017; 17. [PMID: 28613012 DOI: 10.1002/pmic.201600389] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 05/03/2017] [Indexed: 12/19/2022]
Abstract
Remodeling of the extracellular matrix (ECM) is crucial in development and homeostasis, but also has a significant role in disease progression. Two metalloproteinase families, the matrix metalloproteinases (MMPs) and a disintegrin and metalloproteases (ADAMs), participate in the remodeling of the ECM, either directly or through the liberation of growth factors and cell surface receptors. The correlation of MMP and ADAM activity to a variety of diseases has instigated numerous drug development programs. However, broad-based and Zn2+ -chelating MMP and ADAM inhibitors have fared poorly in the clinic. Selective MMP and ADAM inhibitors have been described recently based on (a) antibodies or antibody fragments or (b) small molecules designed to take advantage of protease secondary binding sites (exosites) or allosteric sites. Clinical trials have been undertaken with several of these inhibitors, while others are in advanced pre-clinical stages.
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Affiliation(s)
- Sabrina Amar
- Department of Chemistry & Biochemistry, Florida Atlantic University, Jupiter, FL, USA
| | - Dmitriy Minond
- Rumbaugh-Goodwin Institute for Cancer Research, Nova Southeastern University, Fort Lauderdale, FL, USA
| | - Gregg B Fields
- Department of Chemistry & Biochemistry, Florida Atlantic University, Jupiter, FL, USA.,Department of Chemistry, The Scripps Research Institute/Scripps Florida, Jupiter, FL, USA
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58
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Abstract
Myeloid cells have diverse roles in regulating immunity, inflammation, and extracellular matrix turnover. To accomplish these tasks, myeloid cells carry an arsenal of metalloproteinases, which include the matrix metalloproteinases and the adamalysins. These enzymes have diverse substrate repertoires, and are thus involved in mediating proteolytic cascades, cell migration, and cell signaling. Dysregulation of metalloproteinases contributes to pathogenic processes, including inflammation, fibrosis, and cancer. Metalloproteinases also have important nonproteolytic functions in controlling cytoskeletal dynamics during macrophage fusion and enhancing transcription to promote antiviral immunity. This review highlights the diverse contributions of metalloproteinases to myeloid cell functions.
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59
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Peripheral membrane associations of matrix metalloproteinases. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2017; 1864:1964-1973. [PMID: 28442379 DOI: 10.1016/j.bbamcr.2017.04.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 04/20/2017] [Accepted: 04/20/2017] [Indexed: 12/21/2022]
Abstract
Water soluble matrix metalloproteinases (MMPs) have been regarded as diffusing freely in the extracellular matrix. Yet multiple MMPs are also observed at cell surfaces. Their membrane-proximal activities include sheddase activities, collagenolysis, bacterial killing, and intracellular trafficking reaching as far as the nucleus. The catalytic domains of MMP-7 and MMP-12 bind bilayers peripherally, each in two different orientations, by presenting positive charges and a few hydrophobic groups to the surface. Related peripheral membrane associations are predicted for other soluble MMPs. The peripheral membrane associations may support pericellular proteolysis and endocytosis. The isolated soluble domains of MT1-MMP can also associate with membranes. NMR assays suggest transient association of the hemopexin-like domains of MT1-MMP and MMP-12 with lipid bilayers. Peripheral association of soluble MMP domains with bilayers or heparin sulfate proteoglycans probably concentrates them near the membrane. This could increase the probability of forming complexes with membrane-associated proteins, such as those targeted for proteolysis. This article is part of a Special Issue entitled: Matrix Metalloproteinases edited by Rafael Fridman.
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60
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Wolf M, Maltseva I, Clay SM, Pan P, Gajjala A, Chan MF. Effects of MMP12 on cell motility and inflammation during corneal epithelial repair. Exp Eye Res 2017; 160:11-20. [PMID: 28442300 DOI: 10.1016/j.exer.2017.04.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 03/31/2017] [Accepted: 04/18/2017] [Indexed: 11/25/2022]
Abstract
Corneal epithelial defects are a common cause of ocular morbidity and can result in corneal scarring if they do not heal properly. Matrix metalloproteinases (MMPs) are extracellular matrix proteinases that regulate multiple aspects of corneal repair. We have previously shown that MMP12 has a protective effect on corneal fibrosis through its regulation of neutrophil and macrophage infiltration and angiogenesis in a chemical injury model involving full thickness damage to the cornea. However, the role of MMP12 in injuries limited to the corneal epithelium is relatively unknown. This study investigates the reparative effects of MMP12 following isolated corneal epithelial injury. Using a corneal epithelial debridement injury model performed on corneas of wild-type (WT) mice, we show that Mmp12 is expressed early following corneal epithelial injury with highest expression levels at 8 h after injury and lower expression levels at 4 and 8 days after injury. We investigated whether MMP12 has an effect on the rate of epithelial repair and cell migration using in vivo and in vitro scratch assays performed on WT and Mmp12-/- mice. We found that loss of MMP12 results in a slower scratch wound repair rate both in vivo and in vitro. We also found that corneas of Mmp12-/- mice have decreased neutrophil infiltration following injury. Loss of MMP12, however, does not affect cell proliferation in the center of the wounds. These data support a role of MMP12 in promoting early repair processes following corneal epithelial injury by enhancing epithelial cell migration and neutrophil infiltration.
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Affiliation(s)
- Marie Wolf
- Department of Ophthalmology, University of California, San Francisco, CA, United States
| | - Inna Maltseva
- Department of Anatomy, University of California, San Francisco, CA, United States
| | - Selene M Clay
- Department of Ophthalmology, University of California, San Francisco, CA, United States
| | - Peipei Pan
- Department of Ophthalmology, University of California, San Francisco, CA, United States
| | - Abhinay Gajjala
- University of Rochester School of Medicine and Dentistry, Rochester, NY, United States
| | - Matilda F Chan
- Department of Ophthalmology, University of California, San Francisco, CA, United States; Francis I. Proctor Foundation, University of California, San Francisco, CA, United States.
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Smigiel KS, Parks WC. Matrix Metalloproteinases and Leukocyte Activation. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2017; 147:167-195. [PMID: 28413028 DOI: 10.1016/bs.pmbts.2017.01.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
As their name implies, matrix metalloproteinases (MMPs) are thought to degrade extracellular matrix proteins, a function that is indeed performed by some members. However, regardless of their cell source, matrix degradation is not the only function of these enzymes. Rather, individual MMPs have been shown to regulate specific immune processes, such as leukocyte influx and migration, antimicrobial activity, macrophage activation, and restoration of barrier function, typically by processing a range of nonmatrix protein substrates. Indeed, MMP expression is low under steady-state conditions but is markedly induced during inflammatory processes including infection, wound healing, and cancer. Increasing research is showing that MMPs are not just a downstream consequence of a generalized inflammatory process, but rather are critical factors in the overall regulation of the pattern, type, and duration of immune responses. This chapter outlines the role of leukocytes in tissue remodeling and describes recent progress in our understanding of how MMPs alter leukocyte activity.
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Affiliation(s)
- Kate S Smigiel
- Women's Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - William C Parks
- Women's Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States.
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62
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Taggart C, Mall MA, Lalmanach G, Cataldo D, Ludwig A, Janciauskiene S, Heath N, Meiners S, Overall CM, Schultz C, Turk B, Borensztajn KS. Protean proteases: at the cutting edge of lung diseases. Eur Respir J 2017; 49:49/2/1501200. [PMID: 28179435 DOI: 10.1183/13993003.01200-2015] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 11/27/2016] [Indexed: 12/14/2022]
Abstract
Proteases were traditionally viewed as mere protein-degrading enzymes with a very restricted spectrum of substrates. A major expansion in protease research has uncovered a variety of novel substrates, and it is now evident that proteases are critical pleiotropic actors orchestrating pathophysiological processes. Recent findings evidenced that the net proteolytic activity also relies upon interconnections between different protease and protease inhibitor families in the protease web.In this review, we provide an overview of these novel concepts with a particular focus on pulmonary pathophysiology. We describe the emerging roles of several protease families including cysteine and serine proteases.The complexity of the protease web is exemplified in the light of multidimensional regulation of serine protease activity by matrix metalloproteases through cognate serine protease inhibitor processing. Finally, we will highlight how deregulated protease activity during pulmonary pathogenesis may be exploited for diagnosis/prognosis purposes, and utilised as a therapeutic tool using nanotechnologies.Considering proteases as part of an integrative biology perspective may pave the way for the development of new therapeutic targets to treat pulmonary diseases related to intrinsic protease deregulation.
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Affiliation(s)
- Clifford Taggart
- Airway Innate Immunity Research group (AiiR), Centre for Experimental Medicine, Queen's University Belfast, UK
| | - Marcus A Mall
- Dept of Translational Pulmonology, University of Heidelberg, Heidelberg, Germany.,Division of Pediatric Pulmonology & Allergy and Cystic Fibrosis Center, Dept of Pediatrics, University of Heidelberg, Heidelberg, Germany.,Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany
| | - Gilles Lalmanach
- INSERM UMR1100 Centre d'Etude des Pathologies Respiratoires (CEPR), Equipe: Mécanismes Protéolytiques dans l'Inflammation, Université François Rabelais, Tours, France
| | - Didier Cataldo
- Laboratory of Tumors and Development and Dept of Respiratory Diseases, University of Liege, Liege, Belgium
| | - Andreas Ludwig
- Inflammation Pharmacology Research Group, Institute of Pharmacology and Toxicology, RWTH Aachen University, Aachen, Germany
| | - Sabina Janciauskiene
- Dept of Respiratory Medicine, a member of The German Center for Lung Research (DZL), Hannover Medical School, Hannover, Germany
| | - Nicole Heath
- Division of Pediatric Pulmonology & Allergy and Cystic Fibrosis Center, Dept of Pediatrics, University of Heidelberg, Heidelberg, Germany.,Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany.,European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Silke Meiners
- Comprehensive Pneumology Center (CPC), University Hospital, Ludwig-Maximilians University, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Christopher M Overall
- Centre for Blood Research, Dept of Oral Biological and Medical Research University of British Columbia, Vancouver, BC, Canada
| | - Carsten Schultz
- Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany.,European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Boris Turk
- Dept of Biochemistry & Molecular & Structural Biology, J. Stefan Institute, Ljubljana, Slovenia
| | - Keren S Borensztajn
- INSERM UMR _S933, Université Pierre et Marie Curie, Paris, France .,INSERM UMR1152 Université Paris Diderot, Faculté de Médecine - site Bichat, Paris, France
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63
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Marshall NC, Finlay BB, Overall CM. Sharpening Host Defenses during Infection: Proteases Cut to the Chase. Mol Cell Proteomics 2017; 16:S161-S171. [PMID: 28179412 PMCID: PMC5393396 DOI: 10.1074/mcp.o116.066456] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 02/03/2017] [Indexed: 01/14/2023] Open
Abstract
The human immune system consists of an intricate network of tightly controlled pathways, where proteases are essential instigators and executioners at multiple levels. Invading microbial pathogens also encode proteases that have evolved to manipulate and dysregulate host proteins, including host proteases during the course of disease. The identification of pathogen proteases as well as their substrates and mechanisms of action have empowered significant developments in therapeutics for infectious diseases. Yet for many pathogens, there remains a great deal to be discovered. Recently, proteomic techniques have been developed that can identify proteolytically processed proteins across the proteome. These “degradomics” approaches can identify human substrates of microbial proteases during infection in vivo and expose the molecular-level changes that occur in the human proteome during infection as an operational network to develop hypotheses for further research as well as new therapeutics. This Perspective Article reviews how proteases are utilized during infection by both the human host and invading bacterial pathogens, including archetypal virulence-associated microbial proteases, such as the Clostridia spp. botulinum and tetanus neurotoxins. We highlight the potential knowledge that degradomics studies of host–pathogen interactions would uncover, as well as how degradomics has been successfully applied in similar contexts, including use with a viral protease. We review how microbial proteases have been targeted in current therapeutic approaches and how microbial proteases have shaped and even contributed to human therapeutics beyond infectious disease. Finally, we discuss how, moving forward, degradomics research can greatly contribute to our understanding of how microbial pathogens cause disease in vivo and lead to the identification of novel substrates in vivo, and the development of improved therapeutics to counter these pathogens.
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Affiliation(s)
- Natalie C Marshall
- From the ‡Department of Microbiology & Immunology.,§Michael Smith Laboratories
| | - B Brett Finlay
- From the ‡Department of Microbiology & Immunology.,§Michael Smith Laboratories.,¶Department of Biochemistry & Molecular Biology
| | - Christopher M Overall
- ¶Department of Biochemistry & Molecular Biology, .,**Department of Oral Biological & Medical Sciences, Centre for Blood Research, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
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64
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Differential gene expression in the condylar cartilage of growing rabbits with temporomandibular joint anterior disk displacement—A transcriptomic study. Arch Oral Biol 2017; 74:92-100. [DOI: 10.1016/j.archoralbio.2016.11.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 09/22/2016] [Accepted: 11/04/2016] [Indexed: 12/14/2022]
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65
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Klein T, Viner RI, Overall CM. Quantitative proteomics and terminomics to elucidate the role of ubiquitination and proteolysis in adaptive immunity. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2016; 374:rsta.2015.0372. [PMID: 27644975 PMCID: PMC5031638 DOI: 10.1098/rsta.2015.0372] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 06/27/2016] [Indexed: 06/06/2023]
Abstract
Adaptive immunity is the specialized defence mechanism in vertebrates that evolved to eliminate pathogens. Specialized lymphocytes recognize specific protein epitopes through antigen receptors to mount potent immune responses, many of which are initiated by nuclear factor-kappa B activation and gene transcription. Most, if not all, pathways in adaptive immunity are further regulated by post-translational modification (PTM) of signalling proteins, e.g. phosphorylation, citrullination, ubiquitination and proteolytic processing. The importance of PTMs is reflected by genetic or acquired defects in these pathways that lead to a dysfunctional immune response. Here we discuss the state of the art in targeted proteomics and systems biology approaches to dissect the PTM landscape specifically regarding ubiquitination and proteolysis in B- and T-cell activation. Recent advances have occurred in methods for specific enrichment and targeted quantitation. Together with improved instrument sensitivity, these advances enable the accurate analysis of often rare PTM events that are opaque to conventional proteomics approaches, now rendering in-depth analysis and pathway dissection possible. We discuss published approaches, including as a case study the profiling of the N-terminome of lymphocytes of a rare patient with a genetic defect in the paracaspase protease MALT1, a key regulator protease in antigen-driven signalling, which was manifested by elevated linear ubiquitination.This article is part of the themed issue 'Quantitative mass spectrometry'.
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Affiliation(s)
- Theo Klein
- Centre for Blood Research, University of British Columbia, Vancouver, BC Canada V6T 1Z3 Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC Canada V6T 1Z3 Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC Canada V6T 1Z3
| | - Rosa I Viner
- Thermo Fisher Scientific, San Jose, CA 95134, USA
| | - Christopher M Overall
- Centre for Blood Research, University of British Columbia, Vancouver, BC Canada V6T 1Z3 Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC Canada V6T 1Z3 Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC Canada V6T 1Z3
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66
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Bordenave T, Helle M, Beau F, Georgiadis D, Tepshi L, Bernes M, Ye Y, Levenez L, Poquet E, Nozach H, Razavian M, Toczek J, Stura EA, Dive V, Sadeghi MM, Devel L. Synthesis and in Vitro and in Vivo Evaluation of MMP-12 Selective Optical Probes. Bioconjug Chem 2016; 27:2407-2417. [PMID: 27564088 DOI: 10.1021/acs.bioconjchem.6b00377] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
In designing new tracers consisting of a small peptide conjugated to a reporter of comparable size, particular attention needs to be paid to the selection of the reporter group, which can dictate both the in vitro and the in vivo performances of the whole conjugate. In the case of fluorescent tracers, this is particularly true given the large numbers of available dye moieties differing in their structures and properties. Here, we have investigated the in vitro and in vivo properties of a novel series of MMP-12 selective probes composed of cyanine dyes varying in their structure, net charge, and hydrophilic character, tethered through a linker to a potent and specific MMP-12 phosphinic pseudopeptide inhibitor. The impact of linker length has been also explored. The crystallographic structure of one tracer in complex with MMP-12 has been obtained, providing the first crystal structure of a Cy5.5-derived probe and confirming that the binding of the targeting moiety is unaffected. MMP-12 remains the tracers' privileged target, as attested by their affinity selectivity profile evaluated in solution toward a panel of 12 metalloproteases. In vivo assessment of four selected probes has highlighted not only the impact of the dye structure but also that of the linker length on the probes' blood clearance rates and their biodistributions. These experiments have also provided valuable data on the stability of the dye moieties in vivo. This has permitted the identification of one probe, which combines favorable binding to MMP-12 in solution and on cells with optimized in vivo performance including blood clearance rate suitable for short-time imaging. Through this series of tracers, we have identified various critical factors modulating the tracers' in vivo behavior, which is both useful for the development and optimization of MMP-12 selective radiolabeled tracers and informative for the design of fluorescent probes in general.
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Affiliation(s)
- Thomas Bordenave
- Service d'ingénierie moléculaire des protéines (SIMOPRO), IBITECS, CEA, Université Paris-Saclay , Gif-sur-Yvette F-91191, France
| | - Marion Helle
- Service d'ingénierie moléculaire des protéines (SIMOPRO), IBITECS, CEA, Université Paris-Saclay , Gif-sur-Yvette F-91191, France
| | - Fabrice Beau
- Service d'ingénierie moléculaire des protéines (SIMOPRO), IBITECS, CEA, Université Paris-Saclay , Gif-sur-Yvette F-91191, France
| | - Dimitris Georgiadis
- Department of Chemistry, Laboratory of Organic Chemistry, University of Athens , Panepistimiopolis, Zografou, Athens 15771, Greece
| | - Livia Tepshi
- Service d'ingénierie moléculaire des protéines (SIMOPRO), IBITECS, CEA, Université Paris-Saclay , Gif-sur-Yvette F-91191, France
| | - Mylène Bernes
- Service d'ingénierie moléculaire des protéines (SIMOPRO), IBITECS, CEA, Université Paris-Saclay , Gif-sur-Yvette F-91191, France
| | - Yunpeng Ye
- Cardiovascular Molecular Imaging Laboratory, Section of Cardiovascular Medicine and Yale Cardiovascular Research Center, Yale University School of Medicine , New Haven, Connecticut 06511, United States.,Veterans Affairs Connecticut Healthcare System , West Haven, Connecticut 06516, United States
| | - Laure Levenez
- Service d'ingénierie moléculaire des protéines (SIMOPRO), IBITECS, CEA, Université Paris-Saclay , Gif-sur-Yvette F-91191, France
| | - Enora Poquet
- Service d'ingénierie moléculaire des protéines (SIMOPRO), IBITECS, CEA, Université Paris-Saclay , Gif-sur-Yvette F-91191, France
| | - Hervé Nozach
- Service d'ingénierie moléculaire des protéines (SIMOPRO), IBITECS, CEA, Université Paris-Saclay , Gif-sur-Yvette F-91191, France
| | - Mahmoud Razavian
- Cardiovascular Molecular Imaging Laboratory, Section of Cardiovascular Medicine and Yale Cardiovascular Research Center, Yale University School of Medicine , New Haven, Connecticut 06511, United States.,Veterans Affairs Connecticut Healthcare System , West Haven, Connecticut 06516, United States
| | - Jakub Toczek
- Cardiovascular Molecular Imaging Laboratory, Section of Cardiovascular Medicine and Yale Cardiovascular Research Center, Yale University School of Medicine , New Haven, Connecticut 06511, United States.,Veterans Affairs Connecticut Healthcare System , West Haven, Connecticut 06516, United States
| | - Enrico A Stura
- Service d'ingénierie moléculaire des protéines (SIMOPRO), IBITECS, CEA, Université Paris-Saclay , Gif-sur-Yvette F-91191, France
| | - Vincent Dive
- Service d'ingénierie moléculaire des protéines (SIMOPRO), IBITECS, CEA, Université Paris-Saclay , Gif-sur-Yvette F-91191, France
| | - Mehran M Sadeghi
- Cardiovascular Molecular Imaging Laboratory, Section of Cardiovascular Medicine and Yale Cardiovascular Research Center, Yale University School of Medicine , New Haven, Connecticut 06511, United States.,Veterans Affairs Connecticut Healthcare System , West Haven, Connecticut 06516, United States
| | - Laurent Devel
- Service d'ingénierie moléculaire des protéines (SIMOPRO), IBITECS, CEA, Université Paris-Saclay , Gif-sur-Yvette F-91191, France
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68
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Yuen J, Pluthero FG, Douda DN, Riedl M, Cherry A, Ulanova M, Kahr WHA, Palaniyar N, Licht C. NETosing Neutrophils Activate Complement Both on Their Own NETs and Bacteria via Alternative and Non-alternative Pathways. Front Immunol 2016; 7:137. [PMID: 27148258 PMCID: PMC4831636 DOI: 10.3389/fimmu.2016.00137] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2015] [Accepted: 03/28/2016] [Indexed: 01/28/2023] Open
Abstract
Neutrophils deposit antimicrobial proteins, such as myeloperoxidase and proteases on chromatin, which they release as neutrophil extracellular traps (NETs). Neutrophils also carry key components of the complement alternative pathway (AP) such as properdin or complement factor P (CFP), complement factor B (CFB), and C3. However, the contribution of these complement components and complement activation during NET formation in the presence and absence of bacteria is poorly understood. We studied complement activation on NETs and a Gram-negative opportunistic bacterial pathogen Pseudomonas aeruginosa (PA01, PAKwt, and PAKgfp). Here, we show that anaphylatoxin C5a, formyl-methionyl-leucyl-phenylalanine (fMLP) and phorbol myristate acetate (PMA), which activates NADPH oxidase, induce the release of CFP, CFB, and C3 from neutrophils. In response to PMA or P. aeruginosa, neutrophils secrete CFP, deposit it on NETs and bacteria, and induce the formation of terminal complement complexes (C5b-9). A blocking anti-CFP antibody inhibited AP-mediated but not non-AP-mediated complement activation on NETs and P. aeruginosa. Therefore, NET-mediated complement activation occurs via both AP- and non AP-based mechanisms, and AP-mediated complement activation during NETosis is dependent on CFP. These findings suggest that neutrophils could use their "AP tool kit" to readily activate complement on NETs and Gram-negative bacteria, such as P. aeruginosa, whereas additional components present in the serum help to fix non-AP-mediated complement both on NETs and bacteria. This unique mechanism may play important roles in host defense and help to explain specific roles of complement activation in NET-related diseases.
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Affiliation(s)
- Joshua Yuen
- Cell Biology Program, The Hospital for Sick Children Research Institute, Toronto, ON, Canada; Program in Physiology and Experimental Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Fred G Pluthero
- Cell Biology Program, The Hospital for Sick Children Research Institute, Toronto, ON, Canada; Division of Haematology/Oncology, The Hospital for Sick Children, Toronto, ON, Canada
| | - David N Douda
- Program in Physiology and Experimental Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Magdalena Riedl
- Cell Biology Program, The Hospital for Sick Children Research Institute , Toronto, ON , Canada
| | - Ahmed Cherry
- Cell Biology Program, The Hospital for Sick Children Research Institute , Toronto, ON , Canada
| | - Marina Ulanova
- Division of Medical Sciences, Northern Ontario School of Medicine, Lakehead University , Thunder Bay, ON , Canada
| | - Walter H A Kahr
- Cell Biology Program, The Hospital for Sick Children Research Institute, Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada; Division of Haematology/Oncology, The Hospital for Sick Children, Toronto, ON, Canada; Institute of Medical Sciences, University of Toronto, Toronto, ON, Canada; Department of Biochemistry, University of Toronto, Toronto, ON, Canada; Department of Paediatrics, University of Toronto, Toronto, ON, Canada
| | - Nades Palaniyar
- Program in Physiology and Experimental Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada; Institute of Medical Sciences, University of Toronto, Toronto, ON, Canada
| | - Christoph Licht
- Cell Biology Program, The Hospital for Sick Children Research Institute, Toronto, ON, Canada; Program in Physiology and Experimental Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada; Institute of Medical Sciences, University of Toronto, Toronto, ON, Canada; Department of Paediatrics, University of Toronto, Toronto, ON, Canada; Division of Nephrology, The Hospital for Sick Children, Toronto, ON, Canada
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69
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Eckhard U, Marino G, Butler GS, Overall CM. Positional proteomics in the era of the human proteome project on the doorstep of precision medicine. Biochimie 2016; 122:110-8. [DOI: 10.1016/j.biochi.2015.10.018] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Accepted: 10/28/2015] [Indexed: 12/30/2022]
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70
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Wilson R, Golub SB, Rowley L, Angelucci C, Karpievitch YV, Bateman JF, Fosang AJ. Novel Elements of the Chondrocyte Stress Response Identified Using an in Vitro Model of Mouse Cartilage Degradation. J Proteome Res 2016; 15:1033-50. [PMID: 26794603 DOI: 10.1021/acs.jproteome.5b01115] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The destruction of articular cartilage in osteoarthritis involves chondrocyte dysfunction and imbalanced extracellular matrix (ECM) homeostasis. Pro-inflammatory cytokines such as interleukin-1α (IL-1α) contribute to osteoarthritis pathophysiology, but the effects of IL-1α on chondrocytes within their tissue microenvironment have not been fully evaluated. To redress this we used label-free quantitative proteomics to analyze the chondrocyte response to IL-1α within a native cartilage ECM. Mouse femoral heads were cultured with and without IL-1α, and both the tissue proteome and proteins released into the media were analyzed. New elements of the chondrocyte response to IL-1α related to cellular stress included markers for protein misfolding (Armet, Creld2, and Hyou1), enzymes involved in glutathione biosynthesis and regeneration (Gstp1, Gsto1, and Gsr), and oxidative stress proteins (Prdx2, Txn, Atox1, Hmox1, and Vnn1). Other proteins previously not associated with the IL-1α response in cartilage included ECM components (Smoc2, Kera, and Crispld1) and cysteine proteases (cathepsin Z and legumain), while chondroadherin and cartilage-derived C-type lectin (Clec3a) were identified as novel products of IL-1α-induced cartilage degradation. This first proteome-level view of the cartilage IL-1α response identified candidate biomarkers of cartilage destruction and novel targets for therapeutic intervention in osteoarthritis.
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Affiliation(s)
- Richard Wilson
- Central Science Laboratory, University of Tasmania , Hobart, Tasmania 7001, Australia.,Murdoch Childrens Research Institute, Royal Children's Hospital , Parkville, Melbourne, Victoria 3052, Australia
| | - Suzanne B Golub
- Murdoch Childrens Research Institute, Royal Children's Hospital , Parkville, Melbourne, Victoria 3052, Australia.,Department of Pediatrics, University of Melbourne , Parkville, Victoria 3052, Australia
| | - Lynn Rowley
- Murdoch Childrens Research Institute, Royal Children's Hospital , Parkville, Melbourne, Victoria 3052, Australia
| | - Constanza Angelucci
- Murdoch Childrens Research Institute, Royal Children's Hospital , Parkville, Melbourne, Victoria 3052, Australia
| | - Yuliya V Karpievitch
- School of Physical Sciences, University of Tasmania , Hobart, Tasmania 7001, Australia.,Centre of Excellence in Plant Energy Biology, University of Western Australia and Harry Perkins Institute of Medical Research , Perth, Western Australia 6009, Australia
| | - John F Bateman
- Murdoch Childrens Research Institute, Royal Children's Hospital , Parkville, Melbourne, Victoria 3052, Australia.,Department of Biochemistry and Molecular Biology, University of Melbourne , Parkville, Victoria 3052, Australia
| | - Amanda J Fosang
- Murdoch Childrens Research Institute, Royal Children's Hospital , Parkville, Melbourne, Victoria 3052, Australia.,Department of Pediatrics, University of Melbourne , Parkville, Victoria 3052, Australia
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71
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Prior SH, Fulcher YG, Koppisetti RK, Jurkevich A, Van Doren SR. Charge-Triggered Membrane Insertion of Matrix Metalloproteinase-7, Supporter of Innate Immunity and Tumors. Structure 2015; 23:2099-110. [PMID: 26439767 PMCID: PMC4635031 DOI: 10.1016/j.str.2015.08.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 08/13/2015] [Accepted: 08/24/2015] [Indexed: 02/08/2023]
Abstract
Matrix metalloproteinase-7 (MMP-7) sheds signaling proteins from cell surfaces to activate bacterial killing, wound healing, and tumorigenesis. The mechanism targeting soluble MMP-7 to membranes has been investigated. Nuclear magnetic resonance structures of the zymogen, free and bound to membrane mimics without and with anionic lipid, reveal peripheral binding to bilayers through paramagnetic relaxation enhancements. Addition of cholesterol sulfate partially embeds the protease in the bilayer, restricts its diffusion, and tips the active site away from the bilayer. Its insertion of hydrophobic residues organizes the lipids, pushing the head groups and sterol sulfate outward toward the enzyme's positive charge on the periphery of the enlarged interface. Fluorescence probing demonstrates a similar mode of binding to plasma membranes and internalized vesicles of colon cancer cells. Binding of bilayered micelles induces allosteric activation and conformational change in the auto-inhibitory peptide and the adjacent scissile site, illustrating a potential intermediate in the activation of the zymogen.
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Affiliation(s)
- Stephen H Prior
- Biochemistry Department, University of Missouri, 117 Schweitzer Hall, Columbia, MO 65211, USA
| | - Yan G Fulcher
- Biochemistry Department, University of Missouri, 117 Schweitzer Hall, Columbia, MO 65211, USA
| | - Rama K Koppisetti
- Biochemistry Department, University of Missouri, 117 Schweitzer Hall, Columbia, MO 65211, USA
| | - Alexander Jurkevich
- Molecular Cytology Core, 120 Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Steven R Van Doren
- Biochemistry Department, University of Missouri, 117 Schweitzer Hall, Columbia, MO 65211, USA.
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72
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Wang S, Xu G, Deng L, Gu Z. Transcriptomic study on the impact of temporomandibular joint internal derangement in the condylar cartilage of rabbits. GENOMICS DATA 2015; 5:364-5. [PMID: 26484287 PMCID: PMC4583689 DOI: 10.1016/j.gdata.2015.06.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 06/26/2015] [Accepted: 06/29/2015] [Indexed: 11/30/2022]
Abstract
Internal derangement (ID) in the temporomandibular joint (TMJ) compromises a group of clinical problems, and holds a relative high prevalence in populations. However, the temporal genomic change in gene expression of condylar cartilage during continuous ID remains unclear. Here we reported the differentially expressed gene pattern in condylar cartilage of rabbits with ID from 1 to 8 weeks by microarray analysis. The whole genome project was deposited at GenBank under the accession PRJNA278127. The microarray analysis showed that 6478 genes have more than two-fold changes among all the tested transcripts. Many inflammation gene increased rapidly in the early stage while decrease later. On the contrary, the bone construction related genes showed a low level at first and increased at later period in the ID progression. Besides, the current study found some genes such as HLA2G, which had never been reported, might be relevant with ID.
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Affiliation(s)
- Shuhua Wang
- School of Stomatology, Zhejiang Chinese Medical University, Hangzhou, China
| | - Gaoli Xu
- Department of Oral and Maxillofacial Surgery, School of Stomatology, Zhejiang Chinese Medical University, Hangzhou, China
| | - Liquan Deng
- Key Laboratory of Stomatology, School of Stomatology, Zhejiang Chinese Medical University, Hangzhou, China
| | - Zhiyuan Gu
- School of Stomatology, Zhejiang Chinese Medical University, Hangzhou, China
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73
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Eckhard U, Huesgen PF, Schilling O, Bellac CL, Butler GS, Cox JH, Dufour A, Goebeler V, Kappelhoff R, Keller UAD, Klein T, Lange PF, Marino G, Morrison CJ, Prudova A, Rodriguez D, Starr AE, Wang Y, Overall CM. Active site specificity profiling of the matrix metalloproteinase family: Proteomic identification of 4300 cleavage sites by nine MMPs explored with structural and synthetic peptide cleavage analyses. Matrix Biol 2015; 49:37-60. [PMID: 26407638 DOI: 10.1016/j.matbio.2015.09.003] [Citation(s) in RCA: 134] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 09/17/2015] [Accepted: 09/18/2015] [Indexed: 02/07/2023]
Abstract
Secreted and membrane tethered matrix metalloproteinases (MMPs) are key homeostatic proteases regulating the extracellular signaling and structural matrix environment of cells and tissues. For drug targeting of proteases, selectivity for individual molecules is highly desired and can be met by high yield active site specificity profiling. Using the high throughput Proteomic Identification of protease Cleavage Sites (PICS) method to simultaneously profile both the prime and non-prime sides of the cleavage sites of nine human MMPs, we identified more than 4300 cleavages from P6 to P6' in biologically diverse human peptide libraries. MMP specificity and kinetic efficiency were mainly guided by aliphatic and aromatic residues in P1' (with a ~32-93% preference for leucine depending on the MMP), and basic and small residues in P2' and P3', respectively. A wide differential preference for the hallmark P3 proline was found between MMPs ranging from 15 to 46%, yet when combined in the same peptide with the universally preferred P1' leucine, an unexpected negative cooperativity emerged. This was not observed in previous studies, probably due to the paucity of approaches that profile both the prime and non-prime sides together, and the masking of subsite cooperativity effects by global heat maps and iceLogos. These caveats make it critical to check for these biologically highly important effects by fixing all 20 amino acids one-by-one in the respective subsites and thorough assessing of the inferred specificity logo changes. Indeed an analysis of bona fide MEROPS physiological substrate cleavage data revealed that of the 37 natural substrates with either a P3-Pro or a P1'-Leu only 5 shared both features, confirming the PICS data. Upon probing with several new quenched-fluorescent peptides, rationally designed on our specificity data, the negative cooperativity was explained by reduced non-prime side flexibility constraining accommodation of the rigidifying P3 proline with leucine locked in S1'. Similar negative cooperativity between P3 proline and the novel preference for asparagine in P1 cements our conclusion that non-prime side flexibility greatly impacts MMP binding affinity and cleavage efficiency. Thus, unexpected sequence cooperativity consequences were revealed by PICS that uniquely encompasses both the non-prime and prime sides flanking the proteomic-pinpointed scissile bond.
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Affiliation(s)
- Ulrich Eckhard
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Pitter F Huesgen
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada; Present address: Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Germany
| | - Oliver Schilling
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada; Present address: Institute of Molecular Medicine and Cell Research, University of Freiburg, Freiburg, Germany
| | - Caroline L Bellac
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada; Present address: Swissmedic, Swiss Agency for Therapeutic Products, Bern, Switzerland
| | - Georgina S Butler
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Jennifer H Cox
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada; Present address: Inception Sciences, Vancouver, BC, Canada
| | - Antoine Dufour
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Verena Goebeler
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Reinhild Kappelhoff
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Ulrich Auf dem Keller
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada; Present address: Institute of Molecular Health Sciences, ETH Zürich, Zürich, Switzerland
| | - Theo Klein
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Philipp F Lange
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada; Present address: Department of Pathology, University of British Columbia, Vancouver, BC, Canada
| | - Giada Marino
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Charlotte J Morrison
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada; Present address: Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Anna Prudova
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - David Rodriguez
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada; Present address: Department of Bioquímica y Biología Molecular, Universidad de Oviedo, Oviedo, Spain
| | - Amanda E Starr
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada; Present address: Ottawa Institute of Systems Biology, University of Ottawa, Canada
| | - Yili Wang
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Christopher M Overall
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada.
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74
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Abstract
Hemolytic-uremic syndrome (HUS) is a thrombotic microangiopathy that is characterized by microangiopathic hemolytic anemia, thrombocytopenia, and renal failure. Excess complement activation underlies atypical HUS and is evident in Shiga toxin-induced HUS (STEC-HUS). This Spotlight focuses on new knowledge of the role of Escherichia coli-derived toxins and polyphosphate in modulating complement and coagulation, and how they affect disease progression and response to treatment. Such new insights may impact on current and future choices of therapies for STEC-HUS.
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75
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Eckhard U, Marino G, Abbey SR, Tharmarajah G, Matthew I, Overall CM. The Human Dental Pulp Proteome and N-Terminome: Levering the Unexplored Potential of Semitryptic Peptides Enriched by TAILS to Identify Missing Proteins in the Human Proteome Project in Underexplored Tissues. J Proteome Res 2015; 14:3568-82. [DOI: 10.1021/acs.jproteome.5b00579] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ulrich Eckhard
- 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
| | - Giada Marino
- 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
| | - Simon R. Abbey
- 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
| | - Grace Tharmarajah
- Department
of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Ian Matthew
- Department
of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Christopher M. Overall
- 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
- Department
of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
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76
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Fortelny N, Pavlidis P, Overall CM. The path of no return--Truncated protein N-termini and current ignorance of their genesis. Proteomics 2015; 15:2547-52. [PMID: 26010509 PMCID: PMC4736679 DOI: 10.1002/pmic.201500043] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 04/13/2015] [Accepted: 05/19/2015] [Indexed: 12/30/2022]
Abstract
Almost all regulatory processes in biology ultimately lead to or originate from modifications of protein function. However, it is unclear to which extent each mechanism of regulation actually affects proteins and thus phenotypes. We assessed the extent of N‐terminal protein truncation in a global analysis of N‐terminomics data and find that most proteins have N‐terminally truncated proteoforms. Because N‐terminomics analyses do not identify the process generating the identified N‐termini, we compared identified termini to the three N‐termini generating events: protein cleavage, alternative translation, and alternative splicing. Of these, we sought to identify the most likely cause of N‐terminal protein truncations in the human proteome. We found that protease cleavage and alternative protein translation are the likely cause for most shortened proteoforms. However, the vast majority (about 90%) of N‐termini remain unexplained by any of these processes identified to date, so revealing large gaps in our knowledge of protein termini and their genesis. Further analysis and annotation of terminomics data is required, to which end we have created the TopFIND database, a major systematic annotation effort for protein termini. We outline the new features in version 3.0 of the updated database and the new bioinformatics tools available and encourage submission of generated data to fill current knowledge gaps.
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Affiliation(s)
- Nikolaus Fortelny
- Department of Biochemistry and Molecular Biology, 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, British Columbia, Canada.,Centre for High Throughput Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Paul Pavlidis
- Centre for High Throughput Biology, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Psychiatry, 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.,Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, British, Columbia, Canada.,Centre for Blood Research, University of British Columbia, Vancouver, British Columbia, Canada
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77
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Abstract
Throughout evolution, organisms have developed means to contain wounds by simultaneously limiting bleeding and eliminating pathogens and damaged host cells via the recruitment of innate defense mechanisms. Disease emerges when there is unchecked activation of innate immune and/or coagulation responses. A key component of innate immunity is the complement system. Concurrent excess activation of coagulation and complement - two major blood-borne proteolytic pathways - is evident in numerous diseases, including atherosclerosis, diabetes, venous thromboembolic disease, thrombotic microangiopathies, arthritis, cancer, and infectious diseases. Delineating the cross-talk between these two cascades will uncover novel therapeutic insights.
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Affiliation(s)
- E M Conway
- Centre for Blood Research, Life Sciences Institute, Division of Hematology, Department of Medicine, Faculty of Medicine, University of British Columbia (UBC), Vancouver, BC, Canada
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78
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Schlage P, Kockmann T, Kizhakkedathu JN, auf dem Keller U. Monitoring matrix metalloproteinase activity at the epidermal-dermal interface by SILAC-iTRAQ-TAILS. Proteomics 2015; 15:2491-502. [PMID: 25871442 DOI: 10.1002/pmic.201400627] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2014] [Revised: 02/18/2015] [Accepted: 04/09/2015] [Indexed: 11/07/2022]
Abstract
Secreted proteases act on interstitial tissue secretomes released from multiple cell types. Thus, substrate proteins might be part of higher molecular complexes constituted by many proteins with diverse and potentially unknown cellular origin. In cell culture, these may be reconstituted by mixing native secretomes from different cell types prior to incubation with a test protease. Although current degradomics techniques could identify novel substrate proteins in these complexes, all information on the cellular origin is lost. To address this limitation, we combined iTRAQ-based terminal amine isotopic labeling of substrates (iTRAQ-TAILS) with SILAC to assign proteins to a specific cell type by MS1- and their cleavage by MS2-based quantification in the same experiment. We demonstrate the power of our newly established workflow by monitoring matrix metalloproteinase (MMP) 10 dependent cleavages in mixtures from light-labeled keratinocyte and heavy-labeled fibroblast secretomes. This analysis correctly assigned extracellular matrix components, such as laminins and collagens, to their respective cellular origins and revealed their processing in an MMP10-dependent manner. Hence, our newly devised degradomics workflow facilitates deeper insight into protease activity in complex intercellular compartments such as the epidermal-dermal interface by integrating multiple modes of quantification with positional proteomics. All MS data have been deposited in the ProteomeXchange with identifier PXD001643 (http://proteomecentral.proteomexchange.org/dataset/PXD001643).
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Affiliation(s)
- Pascal Schlage
- Department of Biology, Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Tobias Kockmann
- Department of Biology, Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Jayachandran N Kizhakkedathu
- Centre for Blood Research and Department of Pathology and Laboratory Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Ulrich auf dem Keller
- Department of Biology, Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
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79
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Apte SS, Parks WC. Metalloproteinases: A parade of functions in matrix biology and an outlook for the future. Matrix Biol 2015; 44-46:1-6. [PMID: 25916966 DOI: 10.1016/j.matbio.2015.04.005] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 04/17/2015] [Indexed: 12/13/2022]
Abstract
This issue of Matrix Biology is devoted to exploring how metalloproteinases - here inclusive of related families of extracellular proteinases - act on extracellular matrix (ECM) proteins to influence an astonishing diversity of biological systems and diseases. Since their discovery in the 1960's, matrix metalloproteinases (MMPs) have oft and widely been considered as the principal mediators of ECM destruction. However, as becomes clear from several articles in this issue, MMPs affect processes that both promote and limit ECM assembly, structure, and quantity. Furthermore, it has become increasingly apparent that ECM proteolysis is neither the exclusive function of MMPs nor their only sphere of influence. Thus, other enzymes may be important participants in ECM proteolysis, and indeed they are. The ADAMTS (a disintegrin-like and metalloproteinase domain with thrombospondin type 1 repeat) proteinases, BMP/tolloid proteases, and meprins have all emerged as major mechanisms of ECM proteolysis. An aggregate view of proteolysis as an exquisitely specific and crucial post-translational modification of secreted proteins emerges from these reviews. The cumulative evidence strongly suggests that although some MMPs can and do cleave ECM components, notably fibrillar collagens, the majority of these proteinases are not key physiological participants in morphogenesis nor in control of matrix metabolism in homeostasis or disease. In contrast, deficiency of ADAMTS proteases leads to a remarkable array of morphogenetic defects and connective tissue disorders consistent with a specialized role in turnover of the embryonic provisional ECM and in ECM assembly. Astacin-related proteases emerge into crucial positions in ECM assembly and turnover, although they also have numerous roles related to morphogen and growth factor regulation. To further turn the traditional view on its head, it is clear that many MMPs are key participants in many, diverse immune and inflammation processes rather than ECM proteolysis. The overlap in the activities within and between these families leads to the view that ECM proteolysis, which is indispensable for life, was over-engineered to an extraordinary extent during vertebrate evolution. That these proteinases, which likely evolved within networks regulating morphogenesis, immunity and regeneration, also participate in diseases is a side effect of human longevity. Attempts to inhibit metalloproteinases in human diseases thus require continuing appraisal of their biological roles and cautious evaluation of potential new therapeutic opportunities.
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Affiliation(s)
- Suneel S Apte
- Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA.
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80
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Repnik U, Starr AE, Overall CM, Turk B. Cysteine Cathepsins Activate ELR Chemokines and Inactivate Non-ELR Chemokines. J Biol Chem 2015; 290:13800-11. [PMID: 25833952 DOI: 10.1074/jbc.m115.638395] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Indexed: 12/24/2022] Open
Abstract
Cysteine cathepsins are primarily lysosomal proteases involved in general protein turnover, but they also have specific proteolytic functions in antigen presentation and bone remodeling. Cathepsins are most stable at acidic pH, although growing evidence indicates that they have physiologically relevant activity also at neutral pH. Post-translational proteolytic processing of mature chemokines is a key, yet underappreciated, level of chemokine regulation. Although the role of selected serine proteases and matrix metalloproteases in chemokine processing has long been known, little has been reported about the role of cysteine cathepsins. Here we evaluated cleavage of CXC ELR (CXCL1, -2, -3, -5, and -8) and non-ELR (CXCL9-12) chemokines by cysteine cathepsins B, K, L, and S at neutral pH by high resolution Tris-Tricine SDS-PAGE and matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Whereas cathepsin B cleaved chemokines especially in the C-terminal region, cathepsins K, L, and S cleaved chemokines at the N terminus with glycosaminoglycans modulating cathepsin processing of chemokines. The functional consequences of the cleavages were determined by Ca(2+) mobilization and chemotaxis assays. We show that cysteine cathepsins inactivate and in some cases degrade non-ELR CXC chemokines CXCL9-12. In contrast, cathepsins specifically process ELR CXC chemokines CXCL1, -2, -3, -5, and -8 N-terminally to the ELR motif, thereby generating agonist forms. This study suggests that cysteine cathepsins regulate chemokine activity and thereby leukocyte recruitment during protective or pathological inflammation.
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Affiliation(s)
- Urska Repnik
- From the Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, SI-1000 Ljubljana, Slovenia
| | - Amanda E Starr
- the Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Christopher M Overall
- the Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada, the Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada,
| | - Boris Turk
- From the Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, SI-1000 Ljubljana, Slovenia, the Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, SI-1000 Ljubljana, Slovenia, and the Faculty of Chemistry and Chemical Technology, University of Ljubljana, SI-1000 Ljubljana, Slovenia
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81
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Proteomics beyond large-scale protein expression analysis. Curr Opin Biotechnol 2015; 34:162-70. [PMID: 25636126 DOI: 10.1016/j.copbio.2015.01.005] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 01/14/2015] [Accepted: 01/14/2015] [Indexed: 11/21/2022]
Abstract
Proteomics is commonly referred to as the application of high-throughput approaches to protein expression analysis. Typical results of proteomics studies are inventories of the protein content of a sample or lists of differentially expressed proteins across multiple conditions. Recently, however, an explosion of novel proteomics workflows has significantly expanded proteomics beyond the analysis of protein expression. Targeted proteomics methods, for example, enable the analysis of the fine dynamics of protein systems, such as a specific pathway or a network of interacting proteins, and the determination of protein complex stoichiometries. Structural proteomics tools allow extraction of restraints for structural modeling and identification of structurally altered proteins on a proteome-wide scale. Other variations of the proteomic workflow can be applied to the large-scale analysis of protein activity, location, degradation and turnover. These exciting developments provide new tools for multi-level 'omics' analysis and for the modeling of biological networks in the context of systems biology studies.
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82
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Proteomic approaches to uncover MMP function. Matrix Biol 2015; 44-46:232-8. [PMID: 25603365 DOI: 10.1016/j.matbio.2015.01.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 01/09/2015] [Accepted: 01/09/2015] [Indexed: 12/30/2022]
Abstract
Proteomics has revolutionized protease research and particularly contributed to the identification of novel substrates and their sites of cleavage as key determinants of protease function. New technologies and rapid advancements in development of powerful mass spectrometers allowed unprecedented insights into activities of matrix metalloproteinases (MMPs) within their complex extracellular environments. Mass spectrometry-based proteomics extended our knowledge on MMP cleavage specificities and will help to develop more specific inhibitors as new therapeutics. Quantitative proteomics and N-terminal enrichment strategies have revealed numerous novel MMP substrates and shed light on their modes of action in vitro and in vivo. In this review, we provide an overview of current proteomic technologies in protease research and their application to the functional characterization of MMPs.
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83
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Matrix metalloproteinase interactions with collagen and elastin. Matrix Biol 2015; 44-46:224-31. [PMID: 25599938 PMCID: PMC4466143 DOI: 10.1016/j.matbio.2015.01.005] [Citation(s) in RCA: 237] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 01/10/2015] [Accepted: 01/10/2015] [Indexed: 12/18/2022]
Abstract
Most abundant in the extracellular matrix are collagens, joined by elastin that confers elastic recoil to the lung, aorta, and skin. These fibrils are highly resistant to proteolysis but can succumb to a minority of the matrix metalloproteinases (MMPs). Considerable inroads to understanding how such MMPs move to the susceptible sites in collagen and then unwind the triple helix of collagen monomers have been gained. The essential role in unwinding of the hemopexin-like domain of interstitial collagenases or the collagen binding domain of gelatinases is highlighted. Elastolysis is also facilitated by the collagen binding domain in the cases of MMP-2 and MMP-9, and remote exosites of the catalytic domain in the case of MMP-12.
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84
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Sabino F, Hermes O, Egli FE, Kockmann T, Schlage P, Croizat P, Kizhakkedathu JN, Smola H, auf dem Keller U. In vivo assessment of protease dynamics in cutaneous wound healing by degradomics analysis of porcine wound exudates. Mol Cell Proteomics 2014; 14:354-70. [PMID: 25516628 DOI: 10.1074/mcp.m114.043414] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Proteases control complex tissue responses by modulating inflammation, cell proliferation and migration, and matrix remodeling. All these processes are orchestrated in cutaneous wound healing to restore the skin's barrier function upon injury. Altered protease activity has been implicated in the pathogenesis of healing impairments, and proteases are important targets in diagnosis and therapy of this pathology. Global assessment of proteolysis at critical turning points after injury will define crucial events in acute healing that might be disturbed in healing disorders. As optimal biospecimens, wound exudates contain an ideal proteome to detect extracellular proteolytic events, are noninvasively accessible, and can be collected at multiple time points along the healing process from the same wound in the clinics. In this study, we applied multiplexed Terminal Amine Isotopic Labeling of Substrates (TAILS) to globally assess proteolysis in early phases of cutaneous wound healing. By quantitative analysis of proteins and protein N termini in wound fluids from a clinically relevant pig wound model, we identified more than 650 proteins and discerned major healing phases through distinctive abundance clustering of markers of inflammation, granulation tissue formation, and re-epithelialization. TAILS revealed a high degree of proteolysis at all time points after injury by detecting almost 1300 N-terminal peptides in ∼450 proteins. Quantitative positional proteomics mapped pivotal interdependent processing events in the blood coagulation and complement cascades, temporally discerned clotting and fibrinolysis during the healing process, and detected processing of complement C3 at distinct time points after wounding and by different proteases. Exploiting data on primary cleavage specificities, we related candidate proteases to cleavage events and revealed processing of the integrin adapter protein kindlin-3 by caspase-3, generating new hypotheses for protease-substrate relations in the healing skin wound in vivo. The data have been deposited to the ProteomeXchange Consortium with identifier PXD001198.
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Affiliation(s)
- Fabio Sabino
- From the ‡ETH Zurich, Department of Biology, Institute of Molecular Health Sciences, Otto-Stern-Weg 7, 8093 Zurich, Switzerland
| | - Olivia Hermes
- From the ‡ETH Zurich, Department of Biology, Institute of Molecular Health Sciences, Otto-Stern-Weg 7, 8093 Zurich, Switzerland
| | - Fabian E Egli
- From the ‡ETH Zurich, Department of Biology, Institute of Molecular Health Sciences, Otto-Stern-Weg 7, 8093 Zurich, Switzerland
| | - Tobias Kockmann
- From the ‡ETH Zurich, Department of Biology, Institute of Molecular Health Sciences, Otto-Stern-Weg 7, 8093 Zurich, Switzerland
| | - Pascal Schlage
- From the ‡ETH Zurich, Department of Biology, Institute of Molecular Health Sciences, Otto-Stern-Weg 7, 8093 Zurich, Switzerland
| | - Pierre Croizat
- §Paul Hartmann AG, Paul Hartmann Strasse 12, 89522 Heidenheim, Germany
| | - Jayachandran N Kizhakkedathu
- ¶University of British Columbia, Department of Pathology and Laboratory Medicine and Department of Chemistry, Centre for Blood Research, 4.401 Life Sciences Institute, 2350 Health Sciences Mall, Vancouver, British Columbia, Canada V6T 1Z3
| | - Hans Smola
- §Paul Hartmann AG, Paul Hartmann Strasse 12, 89522 Heidenheim, Germany
| | - Ulrich auf dem Keller
- From the ‡ETH Zurich, Department of Biology, Institute of Molecular Health Sciences, Otto-Stern-Weg 7, 8093 Zurich, Switzerland;
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