1
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Jiang Y, Rex DA, Schuster D, Neely BA, Rosano GL, Volkmar N, Momenzadeh A, Peters-Clarke TM, Egbert SB, Kreimer S, Doud EH, Crook OM, Yadav AK, Vanuopadath M, Hegeman AD, Mayta M, Duboff AG, Riley NM, Moritz RL, Meyer JG. Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry. ACS MEASUREMENT SCIENCE AU 2024; 4:338-417. [PMID: 39193565 PMCID: PMC11348894 DOI: 10.1021/acsmeasuresciau.3c00068] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 05/03/2024] [Accepted: 05/03/2024] [Indexed: 08/29/2024]
Abstract
Proteomics is the large scale study of protein structure and function from biological systems through protein identification and quantification. "Shotgun proteomics" or "bottom-up proteomics" is the prevailing strategy, in which proteins are hydrolyzed into peptides that are analyzed by mass spectrometry. Proteomics studies can be applied to diverse studies ranging from simple protein identification to studies of proteoforms, protein-protein interactions, protein structural alterations, absolute and relative protein quantification, post-translational modifications, and protein stability. To enable this range of different experiments, there are diverse strategies for proteome analysis. The nuances of how proteomic workflows differ may be challenging to understand for new practitioners. Here, we provide a comprehensive overview of different proteomics methods. We cover from biochemistry basics and protein extraction to biological interpretation and orthogonal validation. We expect this Review will serve as a handbook for researchers who are new to the field of bottom-up proteomics.
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Affiliation(s)
- Yuming Jiang
- Department
of Computational Biomedicine, Cedars Sinai
Medical Center, Los Angeles, California 90048, United States
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
| | - Devasahayam Arokia
Balaya Rex
- Center for
Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - Dina Schuster
- Department
of Biology, Institute of Molecular Systems
Biology, ETH Zurich, Zurich 8093, Switzerland
- Department
of Biology, Institute of Molecular Biology
and Biophysics, ETH Zurich, Zurich 8093, Switzerland
- Laboratory
of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, Villigen 5232, Switzerland
| | - Benjamin A. Neely
- Chemical
Sciences Division, National Institute of
Standards and Technology, NIST, Charleston, South Carolina 29412, United States
| | - Germán L. Rosano
- Mass
Spectrometry
Unit, Institute of Molecular and Cellular
Biology of Rosario, Rosario, 2000 Argentina
| | - Norbert Volkmar
- Department
of Biology, Institute of Molecular Systems
Biology, ETH Zurich, Zurich 8093, Switzerland
| | - Amanda Momenzadeh
- Department
of Computational Biomedicine, Cedars Sinai
Medical Center, Los Angeles, California 90048, United States
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
| | - Trenton M. Peters-Clarke
- Department
of Pharmaceutical Chemistry, University
of California—San Francisco, San Francisco, California, 94158, United States
| | - Susan B. Egbert
- Department
of Chemistry, University of Manitoba, Winnipeg, Manitoba, R3T 2N2 Canada
| | - Simion Kreimer
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
| | - Emma H. Doud
- Center
for Proteome Analysis, Indiana University
School of Medicine, Indianapolis, Indiana, 46202-3082, United States
| | - Oliver M. Crook
- Oxford
Protein Informatics Group, Department of Statistics, University of Oxford, Oxford OX1 3LB, United
Kingdom
| | - Amit Kumar Yadav
- Translational
Health Science and Technology Institute, NCR Biotech Science Cluster 3rd Milestone Faridabad-Gurgaon
Expressway, Faridabad, Haryana 121001, India
| | | | - Adrian D. Hegeman
- Departments
of Horticultural Science and Plant and Microbial Biology, University of Minnesota, Twin Cities, Minnesota 55108, United States
| | - Martín
L. Mayta
- School
of Medicine and Health Sciences, Center for Health Sciences Research, Universidad Adventista del Plata, Libertador San Martin 3103, Argentina
- Molecular
Biology Department, School of Pharmacy and Biochemistry, Universidad Nacional de Rosario, Rosario 2000, Argentina
| | - Anna G. Duboff
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Nicholas M. Riley
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Robert L. Moritz
- Institute
for Systems biology, Seattle, Washington 98109, United States
| | - Jesse G. Meyer
- Department
of Computational Biomedicine, Cedars Sinai
Medical Center, Los Angeles, California 90048, United States
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
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2
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Mead TJ, Bhutada S, Foulcer SJ, Peruzzi N, Nelson CM, Seifert DE, Larkin J, Tran-Lundmark K, Filmus J, Apte SS. Combined genetic-pharmacologic inactivation of tightly linked ADAMTS proteases in temporally specific windows uncovers distinct roles for versican proteolysis and glypican-6 in cardiac development. Matrix Biol 2024; 131:1-16. [PMID: 38750698 DOI: 10.1016/j.matbio.2024.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 05/07/2024] [Accepted: 05/09/2024] [Indexed: 05/22/2024]
Abstract
Extracellular matrix remodeling mechanisms are understudied in cardiac development and congenital heart defects. We show that matrix-degrading metalloproteases ADAMTS1 and ADAMTS5, are extensively co-expressed during mouse cardiac development. The mouse mutants of each gene have mild cardiac anomalies, however, their combined genetic inactivation to elicit cooperative roles is precluded by tight gene linkage. Therefore, we coupled Adamts1 inactivation with pharmacologic ADAMTS5 blockade to uncover stage-specific cooperative roles and investigated their potential substrates in mouse cardiac development. ADAMTS5 blockade was achieved in Adamts1 null mouse embryos using an activity-blocking monoclonal antibody during distinct developmental windows spanning myocardial compaction or cardiac septation and outflow tract rotation. Synchrotron imaging, RNA in situ hybridization, immunofluorescence microscopy and electron microscopy were used to determine the impact on cardiac development and compared to Gpc6 and ADAMTS-cleavage resistant versican mutants. Mass spectrometry-based N-terminomics was used to seek relevant substrates. Combined inactivation of ADAMTS1 and ADAMTS5 prior to 12.5 days of gestation led to dramatic accumulation of versican-rich cardiac jelly and inhibited formation of compact and trabecular myocardium, which was also observed in mice with ADAMTS cleavage-resistant versican. Combined inactivation after 12.5 days impaired outflow tract development and ventricular septal closure, generating a tetralogy of Fallot-like defect. N-terminomics of combined ADAMTS knockout and control hearts identified a cleaved glypican-6 peptide only in the controls. ADAMTS1 and ADAMTS5 expression in cells was associated with specific glypican-6 cleavages. Paradoxically, combined ADAMTS1 and ADAMTS5 inactivation reduced cardiac glypican-6 and outflow tract Gpc6 transcription. Notably, Gpc6-/- hearts demonstrated similar rotational defects as combined ADAMTS inactivated hearts and both had reduced hedgehog signaling. Thus, versican proteolysis in cardiac jelly at the canonical Glu441-Ala442 site is cooperatively mediated by ADAMTS1 and ADAMTS5 and required for proper ventricular cardiomyogenesis, whereas, reduced glypican-6 after combined ADAMTS inactivation impairs hedgehog signaling, leading to outflow tract malrotation.
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Affiliation(s)
- Timothy J Mead
- Department of Biomedical Engineering, Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA; Department of Pediatrics, Case Western Reserve University School of Medicine, Cleveland, OH, USA; University Hospitals Rainbow Babies and Children's Hospital, Cleveland, OH, USA.
| | - Sumit Bhutada
- Department of Biomedical Engineering, Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA
| | - Simon J Foulcer
- Department of Biomedical Engineering, Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA
| | - Niccolò Peruzzi
- Department of Experimental Medical Science, and Wallenberg Center for Molecular Medicine Lund University and The Pediatric Heart Center, Skane University Hospital, Lund, Sweden
| | - Courtney M Nelson
- Department of Biomedical Engineering, Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA
| | - Deborah E Seifert
- Department of Pediatrics, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | | | - Karin Tran-Lundmark
- Department of Experimental Medical Science, and Wallenberg Center for Molecular Medicine Lund University and The Pediatric Heart Center, Skane University Hospital, Lund, Sweden
| | - Jorge Filmus
- Sunnybrook Research Institute and Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Suneel S Apte
- Department of Biomedical Engineering, Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA.
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3
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Kalogeropoulos K, Moldt Haack A, Madzharova E, Di Lorenzo A, Hanna R, Schoof EM, Auf dem Keller U. CLIPPER 2.0: Peptide-Level Annotation and Data Analysis for Positional Proteomics. Mol Cell Proteomics 2024; 23:100781. [PMID: 38703894 PMCID: PMC11192779 DOI: 10.1016/j.mcpro.2024.100781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 04/11/2024] [Accepted: 05/01/2024] [Indexed: 05/06/2024] Open
Abstract
Positional proteomics methodologies have transformed protease research, and have brought mass spectrometry (MS)-based degradomics studies to the forefront of protease characterization and system-wide interrogation of protease signaling. Considerable advancements in both sensitivity and throughput of liquid chromatography (LC)-MS/MS instrumentation enable the generation of enormous positional proteomics datasets of natural and protein termini and neo-termini of cleaved protease substrates. However, concomitant progress has not been observed to the same extent in data analysis and post-processing steps, arguably constituting the largest bottleneck in positional proteomics workflows. Here, we present a computational tool, CLIPPER 2.0, that builds on prior algorithms developed for MS-based protein termini analysis, facilitating peptide-level annotation and data analysis. CLIPPER 2.0 can be used with several sample preparation workflows and proteomics search algorithms and enables fast and automated database information retrieval, statistical and network analysis, as well as visualization of terminomic datasets. We demonstrate the applicability of our tool by analyzing GluC and MMP9 cleavages in HeLa lysates. CLIPPER 2.0 is available at https://github.com/UadKLab/CLIPPER-2.0.
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Affiliation(s)
| | - Aleksander Moldt Haack
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark.
| | - Elizabeta Madzharova
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Antea Di Lorenzo
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Rawad Hanna
- Faculty of Biology, Technion-Israel Institute of Technology, Technion City Haifa, Israel
| | - Erwin M Schoof
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Ulrich Auf dem Keller
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
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4
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Demir F, Kizhakkedathu JN, Rinschen MM, Huesgen PF. MANTI: Automated Annotation of Protein N-Termini for Rapid Interpretation of N-Terminome Data Sets. Anal Chem 2021; 93:5596-5605. [PMID: 33729755 PMCID: PMC8027985 DOI: 10.1021/acs.analchem.1c00310] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 03/04/2021] [Indexed: 12/23/2022]
Abstract
Site-specific proteolytic processing is an important, irreversible post-translational protein modification with implications in many diseases. Enrichment of protein N-terminal peptides followed by mass spectrometry-based identification and quantification enables proteome-wide characterization of proteolytic processes and protease substrates but is challenged by the lack of specific annotation tools. A common problem is, for example, ambiguous matches of identified peptides to multiple protein entries in the databases used for identification. We developed MaxQuant Advanced N-termini Interpreter (MANTI), a standalone Perl software with an optional graphical user interface that validates and annotates N-terminal peptides identified by database searches with the popular MaxQuant software package by integrating information from multiple data sources. MANTI utilizes diverse annotation information in a multistep decision process to assign a conservative preferred protein entry for each N-terminal peptide, enabling automated classification according to the likely origin and determines significant changes in N-terminal peptide abundance. Auxiliary R scripts included in the software package summarize and visualize key aspects of the data. To showcase the utility of MANTI, we generated two large-scale TAILS N-terminome data sets from two different animal models of chemically and genetically induced kidney disease, puromycin adenonucleoside-treated rats (PAN), and heterozygous Wilms Tumor protein 1 mice (WT1). MANTI enabled rapid validation and autonomous annotation of >10 000 identified terminal peptides, revealing novel proteolytic proteoforms in 905 and 644 proteins, respectively. Quantitative analysis indicated that proteolytic activities with similar sequence specificity are involved in the pathogenesis of kidney injury and proteinuria in both models, whereas coagulation processes and complement activation were specifically induced after chemical injury.
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Affiliation(s)
- Fatih Demir
- Department
of Biomedicine, Aarhus University, Høegh-Guldbergsgade 10, 8000 Aarhus C, Denmark
- Central
Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum
Jülich GmbH, 52425 Jülich, Germany
| | - Jayachandran N. Kizhakkedathu
- Centre
for Blood Research, Department of Pathology & Laboratory Medicine,
School of Biomedical Engineering, Department of Chemistry, University of British Columbia, 251-2222 Health Sciences Mall, Vancouver V6T 1Z3, British Columbia, Canada
| | - Markus M. Rinschen
- Department
of Biomedicine, Aarhus University, Høegh-Guldbergsgade 10, 8000 Aarhus C, Denmark
- III.
Department of Medicine, University Medical
Center Hamburg-Eppendorf, Martinistraße 52, 20251 Hamburg, Germany
| | - Pitter F. Huesgen
- Central
Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum
Jülich GmbH, 52425 Jülich, Germany
- Cologne
Excellence Cluster Cellular Stress Response in Aging-Associated Diseases
(CECAD), Medical Faculty and University Hospital, Institute of Biochemistry,
Department of Chemistry, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
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5
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Leduc C, Dupont L, Joannes L, Monseur C, Baiwir D, Mazzucchelli G, Deroanne C, Colige A, Bekhouche M. In vivo N-Terminomics Highlights Novel Functions of ADAMTS2 and ADAMTS14 in Skin Collagen Matrix Building. Front Mol Biosci 2021; 8:643178. [PMID: 33816558 PMCID: PMC8017238 DOI: 10.3389/fmolb.2021.643178] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 02/08/2021] [Indexed: 12/12/2022] Open
Abstract
A disintegrin and metalloproteinase with thrombospondin type I motif (ADAMTS)2 and ADAMTS14 were originally known for their ability to cleave the aminopropeptides of fibrillar collagens. Previous work using N-terminomic approach (N-TAILS) in vitro led to the identification of new substrates, including some molecules involved in TGF-β signaling. Here, N-TAILS was used to investigate the substrates of these two enzymes in vivo, by comparing the N-terminomes of the skin of wild type mice, mice deficient in ADAMTS2, in ADAMTS14 and in both ADAMTS2 and ADAMTS14. This study identified 68 potential extracellular and cell surface proteins, with the majority of them being cleaved by both enzymes. These analyses comfort their role in collagen matrix organization and suggest their implication in inflammatory processes. Regarding fibrillar collagen, this study demonstrates that both ADAMTS2 and ADAMTS14 are involved in the processing of the aminopropeptide of alpha1 and alpha2 type V collagen. It also revealed the existence of several cleavage sites in the Col1 domain and in the C-propeptide of type I collagens. In addition to collagens and other extracellular proteins, two major components of the cell cytoskeleton, actin and vimentin, were also identified as potential substrates. The latter data were confirmed in vitro using purified enzymes and could potentially indicate other functions for ADAMTS2 and 14. This original investigation of mouse skin degradomes by N-terminomic highlights the essential role of ADAMTS2 and ADAMTS14 in collagen matrix synthesis and turnover, and gives clues to better understand their functions in skin pathophysiology. Data are available via ProteomeXchange with identifier PXD022179.
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Affiliation(s)
- Cédric Leduc
- Laboratory of Connective Tissues Biology, GIGA-Cancer, University of Liège, Liège, Belgium
| | - Laura Dupont
- Laboratory of Connective Tissues Biology, GIGA-Cancer, University of Liège, Liège, Belgium
| | - Loïc Joannes
- Laboratory of Connective Tissues Biology, GIGA-Cancer, University of Liège, Liège, Belgium
| | - Christine Monseur
- Laboratory of Connective Tissues Biology, GIGA-Cancer, University of Liège, Liège, Belgium
| | - Dominique Baiwir
- GIGA Proteomic Facility, GIGA-Interdisciplinary Cluster for Applied Genoproteomics, University of Liège, Liège, Belgium
| | - Gabriel Mazzucchelli
- GIGA Proteomic Facility, GIGA-Interdisciplinary Cluster for Applied Genoproteomics, University of Liège, Liège, Belgium
| | - Christophe Deroanne
- Laboratory of Connective Tissues Biology, GIGA-Cancer, University of Liège, Liège, Belgium
| | - Alain Colige
- Laboratory of Connective Tissues Biology, GIGA-Cancer, University of Liège, Liège, Belgium
| | - Mourad Bekhouche
- Laboratory of Connective Tissues Biology, GIGA-Cancer, University of Liège, Liège, Belgium.,Tissue Biology and Therapeutic Engineering, Centre National de la Recherche Scientifique/University of Lyon Unité Mixte de Recherche 5305, Lyon, France.,Faculté d'Odontologie de Lyon, Université de Lyon, Université Lyon 1, Lyon, France
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6
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Kaushal P, Lee C. N-terminomics - its past and recent advancements. J Proteomics 2020; 233:104089. [PMID: 33359939 DOI: 10.1016/j.jprot.2020.104089] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 07/22/2020] [Accepted: 12/20/2020] [Indexed: 02/06/2023]
Abstract
N-terminomics is a rapidly evolving branch of proteomics that encompasses the study of protein N-terminal sequence. A proteome-wide collection of such sequences has been widely used to understand the proteolytic cascades and in annotating the genome. Over the last two decades, various N-terminomic strategies have been developed for achieving high sensitivity, greater depth of coverage, and high-throughputness. We, in this review, cover how the field of N-terminomics has evolved to date, including discussion on various sample preparation and N-terminal peptide enrichment strategies. We also compare different N-terminomic methods and highlight their relative benefits and shortcomings in their implementation. In addition, an overview of the currently available bioinformatics tools and data analysis pipelines for the annotation of N-terminomic datasets is also included. SIGNIFICANCE: It has been recognized that proteins undergo several post-translational modifications (PTM), and a number of perturbed biological pathways are directly associated with modifications at the terminal sites of a protein. In this regard, N-terminomics can be applied to generate a proteome-wide landscape of mature N-terminal sequences, annotate their source of generation, and recognize their significance in the biological pathways. Besides, a system-wide study can be used to study complicated proteolytic machinery and protease cleavage patterns for potential therapeutic targets. Moreover, due to unprecedented improvements in the analytical methods and mass spectrometry instrumentation in recent times, the N-terminomic methodologies now offers an unparalleled ability to study proteoforms and their implications in clinical conditions. Such approaches can further be applied for the detection of low abundant proteoforms, annotation of non-canonical protein coding sites, identification of candidate disease biomarkers, and, last but not least, the discovery of novel drug targets.
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Affiliation(s)
- Prashant Kaushal
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Republic of Korea
| | - Cheolju Lee
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Republic of Korea; KHU-KIST Department of Converging Science and Technology, Kyung Hee University, 26 Kyunghee-daero, Dongdaemun-gu, Seoul 02447, Republic of Korea.
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7
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Bundgaard L, Savickas S, Auf dem Keller U. Mapping the N-Terminome in Tissue Biopsies by PCT-TAILS. Methods Mol Biol 2020; 2043:285-296. [PMID: 31463921 DOI: 10.1007/978-1-4939-9698-8_24] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Proteases play pivotal roles in multiple biological processes in all living organisms and are tightly regulated under normal conditions, but alterations in the proteolytic system and uncontrolled protease activity result in multiple pathological conditions. A disease will most often be defined by an ensemble of cleavage events-a proteolytic signature, thus the system-wide study of protease substrates has gained significant attention and identification of disease specific clusters of protease substrates holds great promise as targets for diagnostics and therapy.In this chapter we describe a method that enables fast and reproducible analysis of protease substrates and proteolytic products in an amount of tissue less than the quantity obtained by a standard biopsy. The method combines tissue disruption and protein extraction by pressure cycling technology (PCT), N-terminal enrichment by tandem mass tag (TMT)-terminal amine isotopic labeling of substrates (TAILS), peptide analysis by mass spectrometry (MS), and a general pipeline for interpretation of the data.
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Affiliation(s)
- Louise Bundgaard
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Simonas Savickas
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ulrich Auf dem Keller
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark.
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8
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Niedermaier S, Huesgen PF. Positional proteomics for identification of secreted proteoforms released by site-specific processing of membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:140138. [DOI: 10.1016/j.bbapap.2018.09.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 08/31/2018] [Accepted: 09/13/2018] [Indexed: 02/06/2023]
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9
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Tang J, Wang Y, Li Y, Zhang Y, Zhang R, Xiao Z, Luo Y, Guo X, Tao L, Lou Y, Xue W, Zhu F. Recent Technological Advances in the Mass Spectrometry-based Nanomedicine Studies: An Insight from Nanoproteomics. Curr Pharm Des 2019; 25:1536-1553. [PMID: 31258068 DOI: 10.2174/1381612825666190618123306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 06/11/2019] [Indexed: 11/22/2022]
Abstract
Nanoscience becomes one of the most cutting-edge research directions in recent years since it is gradually matured from basic to applied science. Nanoparticles (NPs) and nanomaterials (NMs) play important roles in various aspects of biomedicine science, and their influences on the environment have caused a whole range of uncertainties which require extensive attention. Due to the quantitative and dynamic information provided for human proteome, mass spectrometry (MS)-based quantitative proteomic technique has been a powerful tool for nanomedicine study. In this article, recent trends of progress and development in the nanomedicine of proteomics were discussed from quantification techniques and publicly available resources or tools. First, a variety of popular protein quantification techniques including labeling and label-free strategies applied to nanomedicine studies are overviewed and systematically discussed. Then, numerous protein profiling tools for data processing and postbiological statistical analysis and publicly available data repositories for providing enrichment MS raw data information sources are also discussed.
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Affiliation(s)
- Jing Tang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 401331, China.,School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing 401331, China
| | - Yunxia Wang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 401331, China
| | - Yi Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 401331, China
| | - Yang Zhang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 401331, China.,School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing 401331, China
| | - Runyuan Zhang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 401331, China
| | - Ziyu Xiao
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 401331, China
| | - Yongchao Luo
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 401331, China
| | - Xueying Guo
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 401331, China
| | - Lin Tao
- Key Laboratory of Elemene Class Anti-cancer Chinese Medicine of Zhejiang Province, School of Medicine, Hangzhou Normal University, Hangzhou 310036, China
| | - Yan Lou
- Zhejiang Provincial Key Laboratory for Drug Clinical Research and Evaluation, The First Affiliated Hospital, Zhejiang University, 79 QingChun Road, Hangzhou, Zhejiang 310000, China
| | - Weiwei Xue
- School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing 401331, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 401331, China.,School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing 401331, China
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10
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Madzharova E, Sabino F, Auf dem Keller U. Exploring Extracellular Matrix Degradomes by TMT-TAILS N-Terminomics. Methods Mol Biol 2019; 1944:115-126. [PMID: 30840238 DOI: 10.1007/978-1-4939-9095-5_8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Global characterization of protein N termini provides valuable information on proteome dynamics and diversity in health and disease. Driven by the progress in mass spectrometry-based proteomics, novel approaches for the dedicated investigation of protein N termini and protease substrates have been recently developed. Terminal amine isotopic labeling of substrates (TAILS) is a quantitative proteomics approach suitable for high-throughput and system-wide profiling of protein N termini in complex biological matrices. TAILS employs isotopic labeling of primary amines of intact proteins in combination with an amine-reactive high molecular weight polymer (HPG-ALD) for depletion of internal tryptic peptides and high enrichment of protein N termini by negative selection. Thereby, TAILS allows simultaneous identification of the natural N termini, protease-generated neo-N termini, and endogenously modified (e.g., acetylated) N termini. In this chapter, we provide a protocol for tandem mass tag (TMT)-TAILS analysis and further discuss specific considerations regarding N-terminome data interpretation using Proteome Discoverer™ software.
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Affiliation(s)
- Elizabeta Madzharova
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Fabio Sabino
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ulrich Auf dem Keller
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark.
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11
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Multidimensional Analysis of Protease Substrates and Their Cellular Origins in Mixed Secretomes from Multiple Cell Types. Methods Mol Biol 2018. [PMID: 28315245 DOI: 10.1007/978-1-4939-6850-3_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Although extracellular proteases are confronted with substrate proteins expressed by multiple cell types in vivo, in most protease substrate discovery approaches, the test protease is exposed to a test proteome (secretome) derived only from a single cell type. This limits the potential substrate space and prohibits the formation of protein complexes constituted of components derived from multiple cellular origins. Mixing of secretomes collected from multiple cell types addresses this issue, but information on the cellular origin of a substrate protein is lost. Here, we describe a protocol and the corresponding data analysis workflow for a multidimensional substrate discovery approach termed SILAC -iTRAQ -TAILS that is based on hyperplexed terminal amine isotopic labeling of substrates (TAILS ), allowing identification of substrates and concomitant assignment to cellular origins in mixed secretomes within the same experiment.
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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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Bachofner M, Speicher T, Bogorad RL, Muzumdar S, Derrer CP, Hürlimann F, Böhm F, Nanni P, Kockmann T, Kachaylo E, Meyer M, Padrissa-Altés S, Graf R, Anderson DG, Koteliansky V, Auf dem Keller U, Werner S. Large-Scale Quantitative Proteomics Identifies the Ubiquitin Ligase Nedd4-1 as an Essential Regulator of Liver Regeneration. Dev Cell 2017; 42:616-625.e8. [PMID: 28890072 DOI: 10.1016/j.devcel.2017.07.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 04/16/2017] [Accepted: 07/26/2017] [Indexed: 01/20/2023]
Abstract
The liver is the only organ in mammals that fully regenerates even after major injury. To identify orchestrators of this regenerative response, we performed quantitative large-scale proteomics analysis of cytoplasmic and nuclear fractions from normal versus regenerating mouse liver. Proteins of the ubiquitin-proteasome pathway were rapidly upregulated after two-third hepatectomy, with the ubiquitin ligase Nedd4-1 being a top hit. In vivo knockdown of Nedd4-1 in hepatocytes through nanoparticle-mediated delivery of small interfering RNA caused severe liver damage and inhibition of cell proliferation after hepatectomy, resulting in liver failure. Mechanistically, we demonstrate that Nedd4-1 is required for efficient internalization of major growth factor receptors involved in liver regeneration and their downstream mitogenic signaling. These results highlight the power of large-scale proteomics to identify key players in liver regeneration and the importance of posttranslational regulation of growth factor signaling in this process. Finally, they identify an essential function of Nedd4-1 in tissue repair.
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Affiliation(s)
- Marc Bachofner
- Department of Biology, Institute of Molecular Health Sciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Tobias Speicher
- Department of Biology, Institute of Molecular Health Sciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Roman L Bogorad
- David H. Koch Institute for Integrative Cancer Research, Department of Chemical Engineering, Division of Health Science Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sukalp Muzumdar
- Department of Biology, Institute of Molecular Health Sciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Carina P Derrer
- Department of Biology, Institute of Molecular Health Sciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Fabrizio Hürlimann
- Department of Biology, Institute of Molecular Health Sciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Friederike Böhm
- Department of Biology, Institute of Molecular Health Sciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Paolo Nanni
- Functional Genomics Center Zürich, University of Zürich/ETH Zürich, 8057 Zürich, Switzerland
| | - Tobias Kockmann
- Department of Biology, Institute of Molecular Health Sciences, ETH Zürich, 8093 Zürich, Switzerland; Functional Genomics Center Zürich, University of Zürich/ETH Zürich, 8057 Zürich, Switzerland
| | - Ekaterina Kachaylo
- Swiss HPB Center, Division of Visceral and Transplantation Surgery, University Hospital Zürich, 8091 Zürich, Switzerland
| | - Michael Meyer
- Department of Biology, Institute of Molecular Health Sciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Susagna Padrissa-Altés
- Department of Biology, Institute of Molecular Health Sciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Rolf Graf
- Swiss HPB Center, Division of Visceral and Transplantation Surgery, University Hospital Zürich, 8091 Zürich, Switzerland
| | - Daniel G Anderson
- David H. Koch Institute for Integrative Cancer Research, Department of Chemical Engineering, Division of Health Science Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Division of Health Science Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Victor Koteliansky
- Skolkovo Institute of Science and Technology, ul. Novaya, d.100, Skolkovo 143025, Russian Federation
| | - Ulrich Auf dem Keller
- Department of Biology, Institute of Molecular Health Sciences, ETH Zürich, 8093 Zürich, Switzerland.
| | - Sabine Werner
- Department of Biology, Institute of Molecular Health Sciences, ETH Zürich, 8093 Zürich, Switzerland.
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Demir F, Niedermaier S, Kizhakkedathu JN, Huesgen PF. Profiling of Protein N-Termini and Their Modifications in Complex Samples. Methods Mol Biol 2017; 1574:35-50. [PMID: 28315242 DOI: 10.1007/978-1-4939-6850-3_4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
Protein N termini are a unique window to the functional state of the proteome, revealing translation initiation sites, co-translation truncation and modification, posttranslational maturation, and further proteolytic processing into different proteoforms with distinct functions. As a direct readout of proteolytic activity, protein N termini further reveal proteolytic regulation of diverse biological processes and provide a route to determine specific substrates and hence the physiological functions for any protease of interest. Here, we describe our current protocol of the successful Terminal Amine Isotope Labeling of Substrates (TAILS) technique, which enriches protein N-terminal peptides from complex proteome samples by negative selection. Genome-encoded N termini, protease-generated neo-N termini, and endogenously modified N termini are all enriched simultaneously. Subsequent mass spectrometric analysis therefore profiles all protein N termini and their modifications present in a complex sample in a single experiment. We further provide a detailed protocol for the TAILS-compatible proteome preparation from plant material and discuss specific considerations for N terminome data analysis and annotation.
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Affiliation(s)
- Fatih Demir
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Wilhelm-Johnen-Str, 52425, Jülich, Germany
| | - Stefan Niedermaier
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Wilhelm-Johnen-Str, 52425, Jülich, Germany
| | - Jayachandran N Kizhakkedathu
- Centre for Blood Research, Department of Pathology & Laboratory Medicine, University of British Columbia, 2350 Health Sciences Mall, Vancouver, Canada, V6T 1Z3
- Department of Chemistry, University of British Columbia, 2350 Health Sciences Mall, Vancouver, Canada, V6T 1Z3
| | - Pitter F Huesgen
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Wilhelm-Johnen-Str, 52425, Jülich, Germany.
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Schlage P, Egli FE, Auf dem Keller U. Time-Resolved Analysis of Matrix Metalloproteinase Substrates in Complex Samples. Methods Mol Biol 2017; 1579:185-198. [PMID: 28299737 DOI: 10.1007/978-1-4939-6863-3_9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Identification of physiological substrates is the key to understanding the pleiotropic functions of matrix metalloproteinases (MMPs) in health and disease. Quantitative mass spectrometry-based proteomics has revolutionized current approaches in protease substrate discovery and helped to unravel many new MMP activities in complex biological systems. Multiplexing further extended the capabilities of these techniques and facilitated more complicated experimental designs that include multiple proteases or monitoring the activity of a single protease at more than one concentration or at multiple time points with a complex test proteome. In this chapter, we provide a protocol for time-resolved iTRAQ-based Terminal Amine Isotopic Labeling of Substrates (TAILS), with the focus on MMP substrate identification and characterization in cell culture supernatants and introduce an automated procedure for the interpretation of time-resolved iTRAQ-TAILS datasets.
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Affiliation(s)
- Pascal Schlage
- ETH Zurich, Department of Biology, Institute of Molecular Health Sciences, Otto-Stern-Weg 7, 8093, Zurich, Switzerland
| | - Fabian E Egli
- ETH Zurich, Department of Biology, Institute of Molecular Health Sciences, Otto-Stern-Weg 7, 8093, Zurich, Switzerland
| | - Ulrich Auf dem Keller
- ETH Zurich, Department of Biology, Institute of Molecular Health Sciences, Otto-Stern-Weg 7, 8093, Zurich, Switzerland.
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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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TAILS N-Terminomics and Proteomics Show Protein Degradation Dominates over Proteolytic Processing by Cathepsins in Pancreatic Tumors. Cell Rep 2016; 16:1762-1773. [PMID: 27477282 DOI: 10.1016/j.celrep.2016.06.086] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 05/31/2016] [Accepted: 06/22/2016] [Indexed: 12/13/2022] Open
Abstract
Deregulated cathepsin proteolysis occurs across numerous cancers, but in vivo substrates mediating tumorigenesis remain ill-defined. Applying 8-plex iTRAQ terminal amine isotopic labeling of substrates (TAILS), a systems-level N-terminome degradomics approach, we identified cathepsin B, H, L, S, and Z in vivo substrates and cleavage sites with the use of six different cathepsin knockout genotypes in the Rip1-Tag2 mouse model of pancreatic neuroendocrine tumorigenesis. Among 1,935 proteins and 1,114 N termini identified by TAILS, stable proteolytic products were identified in wild-type tumors compared with one or more different cathepsin knockouts (17%-44% of 139 cleavages). This suggests a lack of compensation at the substrate level by other cathepsins. The majority of neo-N termini (56%-83%) for all cathepsins was consistent with protein degradation. We validated substrates, including the glycolytic enzyme pyruvate kinase M2 associated with the Warburg effect, the ER chaperone GRP78, and the oncoprotein prothymosin-alpha. Thus, the identification of cathepsin substrates in tumorigenesis improves the understanding of cathepsin functions in normal physiology and cancer.
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Bekhouche M, Leduc C, Dupont L, Janssen L, Delolme F, Vadon-Le Goff S, Smargiasso N, Baiwir D, Mazzucchelli G, Zanella-Cleon I, Dubail J, De Pauw E, Nusgens B, Hulmes DJS, Moali C, Colige A. Determination of the substrate repertoire of ADAMTS2, 3, and 14 significantly broadens their functions and identifies extracellular matrix organization and TGF-β signaling as primary targets. FASEB J 2016; 30:1741-56. [PMID: 26740262 DOI: 10.1096/fj.15-279869] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 12/17/2015] [Indexed: 01/03/2023]
Abstract
A disintegrin and metalloproteinase with thrombospondin type I motif (ADAMTS)2, 3, and 14 are collectively named procollagen N-proteinases (pNPs) because of their specific ability to cleave the aminopropeptide of fibrillar procollagens. Several reports also indicate that they could be involved in other biological processes, such as blood coagulation, development, and male fertility, but the potential substrates associated with these activities remain unknown. Using the recently described N-terminal amine isotopic labeling of substrate approach, we analyzed the secretomes of human fibroblasts and identified 8, 17, and 22 candidate substrates for ADAMTS2, 3, and 14, respectively. Among these newly identified substrates, many are components of the extracellular matrix and/or proteins related to cell signaling such as latent TGF-β binding protein 1, TGF-β RIII, and dickkopf-related protein 3. Candidate substrates for the 3 ADAMTS have been biochemically validated in different contexts, and the implication of ADAMTS2 in the control of TGF-β activity has been further demonstrated in human fibroblasts. Finally, the cleavage site specificity was assessed showing a clear and unique preference for nonpolar or slightly hydrophobic amino acids. This work shows that the activities of the pNPs extend far beyond the classically reported processing of the aminopropeptide of fibrillar collagens and that they should now be considered as multilevel regulators of matrix deposition and remodeling.-Bekhouche, M., Leduc, C., Dupont, L., Janssen, L., Delolme, F., Vadon-Le Goff, S., Smargiasso, N., Baiwir, D., Mazzucchelli, G., Zanella-Cleon, I., Dubail, J., De Pauw, E., Nusgens, B., Hulmes, D. J. S., Moali, C., Colige, A. Determination of the substrate repertoire of ADAMTS2, 3, and 14 significantly broadens their functions and identifies extracellular matrix organization and TGF-β signaling as primary targets.
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Affiliation(s)
- Mourad Bekhouche
- Laboratory of Connective Tissues Biology, University of Liège, Liège, Belgium;
| | - Cedric Leduc
- Laboratory of Connective Tissues Biology, University of Liège, Liège, Belgium
| | - Laura Dupont
- Laboratory of Connective Tissues Biology, University of Liège, Liège, Belgium
| | - Lauriane Janssen
- Laboratory of Connective Tissues Biology, University of Liège, Liège, Belgium
| | - Frederic Delolme
- Tissue Biology and Therapeutic Engineering, Centre National de la Recherche Scientifique/University of Lyon Unité Mixte de Recherche 5305, Lyon, France; and Protein Science Facility, Institute for the Biology and Chemistry of Proteins, Unité Mixte de Service 3444, Lyon, France
| | - Sandrine Vadon-Le Goff
- Tissue Biology and Therapeutic Engineering, Centre National de la Recherche Scientifique/University of Lyon Unité Mixte de Recherche 5305, Lyon, France; and
| | - Nicolas Smargiasso
- Mass Spectrometry Laboratory, GIGA Proteomics, University of Liège, Liège, Belgium
| | - Dominique Baiwir
- GIGA Proteomic Facility, GIGA-Interdisciplinary Cluster for Applied Genoproteomics, University of Liège, Liège, Belgium
| | - Gabriel Mazzucchelli
- Mass Spectrometry Laboratory, GIGA Proteomics, University of Liège, Liège, Belgium
| | - Isabelle Zanella-Cleon
- Protein Science Facility, Institute for the Biology and Chemistry of Proteins, Unité Mixte de Service 3444, Lyon, France
| | - Johanne Dubail
- Laboratory of Connective Tissues Biology, University of Liège, Liège, Belgium
| | - Edwin De Pauw
- Mass Spectrometry Laboratory, GIGA Proteomics, University of Liège, Liège, Belgium
| | - Betty Nusgens
- Laboratory of Connective Tissues Biology, University of Liège, Liège, Belgium
| | - David J S Hulmes
- Tissue Biology and Therapeutic Engineering, Centre National de la Recherche Scientifique/University of Lyon Unité Mixte de Recherche 5305, Lyon, France; and
| | - Catherine Moali
- Tissue Biology and Therapeutic Engineering, Centre National de la Recherche Scientifique/University of Lyon Unité Mixte de Recherche 5305, Lyon, France; and
| | - Alain Colige
- Laboratory of Connective Tissues Biology, University of Liège, Liège, Belgium;
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Schlage P, Kockmann T, Sabino F, Kizhakkedathu JN, Auf dem Keller U. Matrix Metalloproteinase 10 Degradomics in Keratinocytes and Epidermal Tissue Identifies Bioactive Substrates With Pleiotropic Functions. Mol Cell Proteomics 2015; 14:3234-46. [PMID: 26475864 DOI: 10.1074/mcp.m115.053520] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Indexed: 01/29/2023] Open
Abstract
Matrix metalloproteinases (MMPs) are important players in skin homeostasis, wound repair, and in the pathogenesis of skin cancer. It is now well established that most of their functions are related to processing of bioactive proteins rather than components of the extracellular matrix (ECM). MMP10 is highly expressed in keratinocytes at the wound edge and at the invasive front of tumors, but hardly any non-ECM substrates have been identified and its function in tissue repair and carcinogenesis is unclear. To better understand the role of MMP10 in the epidermis, we employed multiplexed iTRAQ-based Terminal Amine Isotopic Labeling of Substrates (TAILS) and monitored MMP10-dependent proteolysis over time in secretomes from keratinocytes. Time-resolved abundance clustering of neo-N termini classified MMP10-dependent cleavage events by efficiency and refined the MMP10 cleavage site specificity by revealing a so far unknown preference for glutamate in the P1 position. Moreover, we identified and validated the integrin alpha 6 subunit, cysteine-rich angiogenic inducer 61 and dermokine as novel direct MMP10 substrates and provide evidence for MMP10-dependent but indirect processing of phosphatidylethanolamine-binding protein 1. Finally, we sampled the epidermal proteome and degradome in unprecedented depth and confirmed MMP10-dependent processing of dermokine in vivo by TAILS analysis of epidermis from transgenic mice that overexpress a constitutively active mutant of MMP10 in basal keratinocytes. The newly identified substrates are involved in cell adhesion, migration, proliferation, and/or differentiation, indicating a contribution of MMP10 to local modulation of these processes during wound healing and cancer development. Data are available via ProteomeXchange with identifier PXD002474.
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Affiliation(s)
- Pascal Schlage
- 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
| | - Fabio Sabino
- From the ‡ETH Zurich, Department of Biology,Institute of Molecular Health Sciences, Otto-Stern-Weg 7, 8093 Zurich, Switzerland
| | - Jayachandran N Kizhakkedathu
- §University of British Columbia, Department of Pathology and Laboratory Medicine and Department of Chemistry, Centre for Blood Research, 4.401Life Sciences Institute, 2350 Health Sciences Mall, Vancouver, British Columbia, Canada V6T 1Z3
| | - 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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Eckhard U, Marino G, Abbey SR, Matthew I, Overall CM. TAILS N-terminomic and proteomic datasets of healthy human dental pulp. Data Brief 2015; 5:542-8. [PMID: 26587561 PMCID: PMC4625376 DOI: 10.1016/j.dib.2015.10.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 10/03/2015] [Accepted: 10/06/2015] [Indexed: 11/04/2022] Open
Abstract
The Data described here provide the in depth proteomic assessment of the human dental pulp proteome and N-terminome (Eckhard et al., 2015) [1]. A total of 9 human dental pulps were processed and analyzed by the positional proteomics technique TAILS (Terminal Amine Isotopic Labeling of Substrates) N-terminomics. 38 liquid chromatography tandem mass spectrometry (LC-MS/MS) datasets were collected and analyzed using four database search engines in combination with statistical downstream evaluation, to yield the by far largest proteomic and N-terminomic dataset of any dental tissue to date. The raw mass spectrometry data and the corresponding metadata have been deposited in ProteomeXchange with the PXD identifier <PXD002264>; Supplementary Tables described in this article are available via Mendeley Data (10.17632/555j3kk4sw.1).
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Affiliation(s)
- Ulrich Eckhard
- Centre for Blood Research, The Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada ; Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC, Canada
| | - Giada Marino
- Centre for Blood Research, The Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada ; Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC, Canada
| | - Simon R Abbey
- Centre for Blood Research, The Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada ; Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC, Canada
| | - Ian Matthew
- Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC, Canada
| | - Christopher M Overall
- Centre for Blood Research, The Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada ; Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC, Canada ; Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
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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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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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Identification of Protease Substrates in Complex Proteomes by iTRAQ-TAILS on a Thermo Q Exactive Instrument. ANALYSIS OF POST-TRANSLATIONAL MODIFICATIONS AND PROTEOLYSIS IN NEUROSCIENCE 2015. [DOI: 10.1007/7657_2015_92] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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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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Bellac CL, Dufour A, Krisinger MJ, Loonchanta A, Starr AE, Auf dem Keller U, Lange PF, Goebeler V, Kappelhoff R, Butler GS, Burtnick LD, Conway EM, Roberts CR, Overall CM. Macrophage matrix metalloproteinase-12 dampens inflammation and neutrophil influx in arthritis. Cell Rep 2014; 9:618-32. [PMID: 25310974 DOI: 10.1016/j.celrep.2014.09.006] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Revised: 07/02/2014] [Accepted: 09/02/2014] [Indexed: 12/18/2022] Open
Abstract
Resolution of inflammation reduces pathological tissue destruction and restores tissue homeostasis. Here, we used a proteomic protease substrate discovery approach, terminal amine isotopic labeling of substrates (TAILS), to analyze the role of the macrophage-specific matrix metalloproteinase-12 (MMP12) in inflammation. In murine peritonitis, MMP12 inactivates antithrombin and activates prothrombin, prolonging the activated partial thromboplastin time. Furthermore, MMP12 inactivates complement C3 to reduce complement activation and inactivates the chemoattractant anaphylatoxins C3a and C5a, whereas iC3b and C3b opsonin cleavage increases phagocytosis. Loss of these anti-inflammatory activities in collagen-induced arthritis in Mmp12(-/-) mice leads to unresolved synovitis and extensive articular inflammation. Deep articular cartilage loss is associated with massive neutrophil infiltration and abnormal DNA neutrophil extracellular traps (NETs). The NETs are rich in fibrin and extracellular actin, which TAILS identified as MMP12 substrates. Thus, macrophage MMP12 in arthritis has multiple protective roles in countering neutrophil infiltration, clearing NETs, and dampening inflammatory pathways to prepare for the resolution of inflammation.
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Affiliation(s)
- Caroline L Bellac
- Centre for Blood Research, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Antoine Dufour
- Centre for Blood Research, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Michael J Krisinger
- Centre for Blood Research, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Medicine, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Anantasak Loonchanta
- Centre for Blood Research, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Medicine, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Amanda E Starr
- Centre for Blood Research, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Ulrich Auf dem Keller
- Centre for Blood Research, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Philipp F Lange
- Centre for Blood Research, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Verena Goebeler
- Centre for Blood Research, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Reinhild Kappelhoff
- Centre for Blood Research, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Georgina S Butler
- Centre for Blood Research, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Leslie D Burtnick
- Centre for Blood Research, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Edward M Conway
- Centre for Blood Research, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Medicine, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Clive R Roberts
- Centre for Blood Research, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Christopher M Overall
- Centre for Blood Research, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
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27
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Marchant DJ, Bellac CL, Moraes TJ, Wadsworth SJ, Dufour A, Butler GS, Bilawchuk LM, Hendry RG, Robertson AG, Cheung CT, Ng J, Ang L, Luo Z, Heilbron K, Norris MJ, Duan W, Bucyk T, Karpov A, Devel L, Georgiadis D, Hegele RG, Luo H, Granville DJ, Dive V, McManus BM, Overall CM. A new transcriptional role for matrix metalloproteinase-12 in antiviral immunity. Nat Med 2014; 20:493-502. [DOI: 10.1038/nm.3508] [Citation(s) in RCA: 192] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 02/12/2014] [Indexed: 02/02/2023]
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Schlage P, Egli FE, Nanni P, Wang LW, Kizhakkedathu JN, Apte SS, auf dem Keller U. Time-resolved analysis of the matrix metalloproteinase 10 substrate degradome. Mol Cell Proteomics 2013; 13:580-93. [PMID: 24281761 DOI: 10.1074/mcp.m113.035139] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Proteolysis is an irreversible post-translational modification that affects intra- and intercellular communication by modulating the activity of bioactive mediators. Key to understanding protease function is the system-wide identification of cleavage events and their dynamics in physiological contexts. Despite recent advances in mass spectrometry-based proteomics for high-throughput substrate screening, current approaches suffer from high false positive rates and only capture single states of protease activity. Here, we present a workflow based on multiplexed terminal amine isotopic labeling of substrates for time-resolved substrate degradomics in complex proteomes. This approach significantly enhances confidence in substrate identification and categorizes cleavage events by specificity and structural accessibility of the cleavage site. We demonstrate concomitant quantification of cleavage site spanning peptides and neo-N and/or neo-C termini to estimate relative ratios of noncleaved and cleaved forms of substrate proteins. By applying this strategy to dissect the matrix metalloproteinase 10 (MMP10) substrate degradome in fibroblast secretomes, we identified the extracellular matrix protein ADAMTS-like protein 1 (ADAMTSL1) as a direct MMP10 substrate and revealed MMP10-dependent ectodomain shedding of platelet-derived growth factor receptor alpha (PDGFRα) as well as sequential processing of type I collagen. The data have been deposited to the ProteomeXchange Consortium with identifier PXD000503.
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Affiliation(s)
- Pascal Schlage
- ETH Zurich, Department of Biology, Institute of Molecular Health Sciences, Schafmattstr. 22, 8093 Zurich, Switzerland
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Butler GS, Overall CM. Matrix metalloproteinase processing of signaling molecules to regulate inflammation. Periodontol 2000 2013; 63:123-48. [DOI: 10.1111/prd.12035] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/19/2013] [Indexed: 12/12/2022]
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30
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Differential isotope dansylation labeling combined with liquid chromatography mass spectrometry for quantification of intact and N-terminal truncated proteins. Anal Chim Acta 2013; 792:79-85. [DOI: 10.1016/j.aca.2013.05.065] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Revised: 05/14/2013] [Accepted: 05/22/2013] [Indexed: 11/19/2022]
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Rogers LD, Overall CM. Proteolytic post-translational modification of proteins: proteomic tools and methodology. Mol Cell Proteomics 2013; 12:3532-42. [PMID: 23887885 DOI: 10.1074/mcp.m113.031310] [Citation(s) in RCA: 116] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Proteolytic processing is a ubiquitous and irreversible post-translational modification involving limited and highly specific hydrolysis of peptide and isopeptide bonds of a protein by a protease. Cleavage generates shorter protein chains displaying neo-N and -C termini, often with new or modified biological activities. Within the past decade, degradomics and terminomics have emerged as significant proteomics subfields dedicated to characterizing proteolysis products as well as natural protein N and C termini. Here we provide an overview of contemporary proteomics-based methods, including specific quantitation, data analysis, and curation considerations, and highlight exciting new and emerging applications within these fields enabling in vivo analysis of proteolytic events.
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Affiliation(s)
- Lindsay D Rogers
- Department of Biochemistry and Molecular Biology, Department of Oral Biological and Medical Sciences, and Centre for Blood Research, University of British Columbia, 4.401 Life Sciences Institute, 2350 Health Sciences Mall, Vancouver, British Columbia, V6T 1Z3, Canada
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Wilson CH, Indarto D, Doucet A, Pogson LD, Pitman MR, McNicholas K, Menz RI, Overall CM, Abbott CA. Identifying natural substrates for dipeptidyl peptidases 8 and 9 using terminal amine isotopic labeling of substrates (TAILS) reveals in vivo roles in cellular homeostasis and energy metabolism. J Biol Chem 2013; 288:13936-13949. [PMID: 23519473 PMCID: PMC3656252 DOI: 10.1074/jbc.m112.445841] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Dipeptidyl peptidases (DP) 8 and 9 are homologous, cytoplasmic N-terminal post-proline-cleaving enzymes that are anti-targets for the development of DP4 (DPPIV/CD26) inhibitors for treating type II diabetes. To date, DP8 and DP9 have been implicated in immune responses and cancer biology, but their pathophysiological functions and substrate repertoire remain unknown. This study utilizes terminal amine isotopic labeling of substrates (TAILS), an N-terminal positional proteomic approach, for the discovery of in vivo DP8 and DP9 substrates. In vivo roles for DP8 and DP9 in cellular metabolism and homeostasis were revealed via the identification of more than 29 candidate natural substrates and pathways affected by DP8/DP9 overexpression. Cleavage of 14 substrates was investigated in vitro; 9/14 substrates for both DP8 and DP9 were confirmed by MALDI-TOF MS, including two of high confidence, calreticulin and adenylate kinase 2. Adenylate kinase 2 plays key roles in cellular energy and nucleotide homeostasis. These results demonstrate remarkable in vivo substrate overlap between DP8/DP9, suggesting compensatory roles for these enzymes. This work provides the first global investigation into DP8 and DP9 substrates, providing a number of leads for future investigations into the biological roles and significance of DP8 and DP9 in human health and disease.
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Affiliation(s)
- Claire H Wilson
- School of Biological Sciences, Flinders University, Adelaide, South Australia 5001, Australia; Departments of Biochemistry and Molecular Biology and Oral Biological and Medical Sciences, Centre for Blood Research and Faculty Dentistry, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Dono Indarto
- School of Biological Sciences, Flinders University, Adelaide, South Australia 5001, Australia; Flinders Centre for Innovation in Cancer, Flinders University, Adelaide, South Australia 5001, Australia
| | - Alain Doucet
- Departments of Biochemistry and Molecular Biology and Oral Biological and Medical Sciences, Centre for Blood Research and Faculty Dentistry, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Lisa D Pogson
- School of Biological Sciences, Flinders University, Adelaide, South Australia 5001, Australia; Flinders Centre for Innovation in Cancer, Flinders University, Adelaide, South Australia 5001, Australia
| | - Melissa R Pitman
- School of Biological Sciences, Flinders University, Adelaide, South Australia 5001, Australia
| | - Kym McNicholas
- School of Biological Sciences, Flinders University, Adelaide, South Australia 5001, Australia
| | - R Ian Menz
- School of Biological Sciences, Flinders University, Adelaide, South Australia 5001, Australia
| | - Christopher M Overall
- Departments of Biochemistry and Molecular Biology and Oral Biological and Medical Sciences, Centre for Blood Research and Faculty Dentistry, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.
| | - Catherine A Abbott
- School of Biological Sciences, Flinders University, Adelaide, South Australia 5001, Australia; Flinders Centre for Innovation in Cancer, Flinders University, Adelaide, South Australia 5001, Australia.
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auf dem Keller U, Prudova A, Eckhard U, Fingleton B, Overall CM. Systems-level analysis of proteolytic events in increased vascular permeability and complement activation in skin inflammation. Sci Signal 2013; 6:rs2. [PMID: 23322905 DOI: 10.1126/scisignal.2003512] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
During inflammation, vascular permeability is increased by various proteolytic events, such as the generation of bradykinin, that augment local tissue responses by enabling tissue penetration of serum proteins, including complement and acute-phase proteins. Proteases also govern inflammatory responses by processing extracellular matrix proteins and soluble bioactive mediators. We quantified changes in the proteome and the nature of protein amino termini (the N-terminome) and the altered abundance of murine proteases and inhibitors during skin inflammation. Through analysis of the N-terminome by iTRAQ-TAILS, we identified cotranslational and posttranslational αN-acetylation motifs, quantitative increases in protein abundance, and qualitative changes in the proteolytic signature during inflammation. Of the proteins identified in normal skin, about half were cleaved, and phorbol ester-induced inflammation increased the proportion of cleaved proteins, including chemokines and complement proteins, that were processed at previously uncharacterized sites. In response to phorbol ester-induced inflammation, mice deficient in matrix metalloproteinase 2 (MMP2) showed reduced accumulation of serum proteins in the skin and exhibited different proteolytic networks from those of wild-type mice. We found that the complement 1 (C1) inhibitor attenuated the increase in serum protein accumulation in inflamed skin. Cleavage and inactivation of the C1 inhibitor by MMP2 increased complement activation and bradykinin generation in wild-type mice, leading to increased vessel permeability during inflammation, which was diminished in Mmp2(-/-) mice. Thus, our systems-level analysis of proteolysis dissected cleavage events associated with skin inflammation and demonstrated that loss of a single protease could perturb the proteolytic signaling network and enhance inflammation.
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Affiliation(s)
- Ulrich auf dem Keller
- Department of Oral Biological and Medical Sciences, 4.401 Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada
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