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Zhang Y, Han Y, Zhu W, Yuan J, Liu X. Negative enrichment strategy combined with site-specific derivatization for the C-terminomics. J Proteomics 2023; 287:104978. [PMID: 37507008 DOI: 10.1016/j.jprot.2023.104978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/12/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023]
Abstract
Protein C-termini containing valuable biological information plays a vital role in various physiological processes, such as protein localization, protein recognition, and signal transduction in organisms. However, C-terminal peptide identification is still challenging due to their low abundance and similar physicochemical properties to other digested peptides. Herein, we developed a simple and mild strategy for the enrichment of C-terminal peptides that incorporates selectively 2-pyridinecarbaldehyde (2-PCA) derivatization of α-amine with negative enrichment by NHS resin. Two synthesized peptides were utilized to evaluate the efficiency of 2-PCA derivatization and optimize the coupling conditions of NHS resin. The feasibility of the method was further validated by enriching the C-terminus of the bovine serum albumin (BSA). Finally, this method was successfully applied to the C-terminus analysis of mouse brain tissue, identifying 404 protein C-termini with physicochemical properties unbiasedly. Additionally, the GO and KEGG analyses revealed that these identified proteins are crucial for proper brain function. In summary, our proposed method is effective and has the potential to facilitate comprehensive C-terminal analysis of proteins. SIGNIFICANCE: Effective enrichment methods are essential for the identification of the proteins C-terminus. In this study, a mild and simple method for negative C-terminal enrichment combined with site-specific derivatization was developed. The enrichment process was simplified and minimized sample loss simultaneously, using 2-PCA derivatization which has high α-amino specificity. Up to 346C-terminal proteins were identified in mouse brain tissue unbiasedly and reliably. This approach has the potential to facilitate comprehensive analysis of protein C-termini in a variety of biological contexts.
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Affiliation(s)
- Yuanyuan Zhang
- Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Yutong Han
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Innovation Institute, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Wenjie Zhu
- Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Jing Yuan
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Innovation Institute, Huazhong University of Science and Technology, Wuhan 430074, China..
| | - Xin Liu
- Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.
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2
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Lange PF, Schilling O, Huesgen PF. Positional proteomics: is the technology ready to study clinical cohorts? Expert Rev Proteomics 2023; 20:309-318. [PMID: 37869791 DOI: 10.1080/14789450.2023.2272046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 08/22/2023] [Indexed: 10/24/2023]
Abstract
INTRODUCTION Positional proteomics provides proteome-wide information on protein termini and their modifications, uniquely enabling unambiguous identification of site-specific, limited proteolysis. Such proteolytic cleavage irreversibly modifies protein sequences resulting in new proteoforms with distinct protease-generated neo-N and C-termini and altered localization and activity. Misregulated proteolysis is implicated in a wide variety of human diseases. Protein termini, therefore, constitute a huge, largely unexplored source of specific analytes that provides a deep view into the functional proteome and a treasure trove for biomarkers. AREAS COVERED We briefly review principal approaches to define protein termini and discuss recent advances in method development. We further highlight the potential of positional proteomics to identify and trace specific proteoforms, with a focus on proteolytic processes altered in disease. Lastly, we discuss current challenges and potential for applying positional proteomics in biomarker and pre-clinical research. EXPERT OPINION Recent developments in positional proteomics have provided significant advances in sensitivity and throughput. In-depth analysis of proteolytic processes in clinical cohorts thus appears feasible in the near future. We argue that this will provide insights into the functional state of the proteome and offer new opportunities to utilize proteolytic processes altered or targeted in disease as specific diagnostic, prognostic and companion biomarkers.
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Affiliation(s)
- Philipp F Lange
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
- Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital Research Institute, Vancouver, BC, Canada
- Department of Molecular Oncology, BC Cancer Research Centre, Vancouver, BC, Canada
| | - Oliver Schilling
- Institute of Surgical Pathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Pitter F Huesgen
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Jülich, Germany
- Cologne Excellence Cluster on Stress Responses in Ageing-Associated Diseases, CECAD, Medical Faculty and University Hospital, University of Cologne, Cologne, Germany
- Institute of Biochemistry, Department for Chemistry, University of Cologne, Cologne, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
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3
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Richert R, Ducret M, Alliot-Licht B, Bekhouche M, Gobert S, Farges JC. A critical analysis of research methods and experimental models to study pulpitis. Int Endod J 2022; 55 Suppl 1:14-36. [PMID: 35034368 DOI: 10.1111/iej.13683] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 01/10/2022] [Accepted: 01/11/2022] [Indexed: 11/29/2022]
Abstract
Pulpitis is the inflammatory response of the dental pulp to a tooth insult, whether it is microbial, chemical, or physical in origin. It is traditionally referred to as reversible or irreversible, a classification for therapeutic purposes that determines the capability of the pulp to heal. Recently, new knowledge about dental pulp physiopathology led to orientate therapeutics towards more frequent preservation of pulp vitality. However, full adoption of these vital pulp therapies by dental practitioners will be achieved only following better understanding of cell and tissue mechanisms involved in pulpitis. The current narrative review aimed to discuss the contribution of the most significant experimental models developed to study pulpitis. Traditionally, in vitro two(2D)- or three(3D)-dimensional cell cultures or in vivo animal models were used to analyse the pulp response to pulpitis inducers at cell, tissue or organ level. In vitro 2D cell cultures were mainly used to decipher the specific roles of key actors of pulp inflammation such as bacterial by-products, pro-inflammatory cytokines, odontoblasts or pulp stem cells. However, these simple models did not reproduce the 3D organisation of the pulp tissue and, with rare exceptions, did not consider interactions between resident cell types. In vitro tissue/organ-based models were developed to better reflect the complexity of the pulp structure. Their major disadvantage is that they did not allow the analysis of blood supply and innervation participation. On the contrary, in vivo models have allowed researchers to identify key immune, vascular and nervous actors of pulpitis and to understand their function and interplay in the inflamed pulp. However, inflammation was mainly induced by iatrogenic dentine drilling associated with simple pulp exposure to the oral environment or stimulation by individual bacterial by-products for short periods. Clearly, these models did not reflect the long and progressive development of dental caries. Lastly, the substantial diversity of the existing models makes experimental data extrapolation to the clinical situation complicated. Therefore, improvement in the design and standardization of future models, for example by using novel molecular biomarkers, databased models and artificial intelligence, will be an essential step in building an incremental knowledge of pulpitis in the future.
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Affiliation(s)
- Raphaël Richert
- Hospices Civils de Lyon, Service d'Odontologie, Lyon, France.,Université de Lyon, Université Claude Bernard Lyon 1, Faculté d'Odontologie, Lyon, France.,Laboratoire de Mécanique des Contacts et Structures, UMR 5259, Villeurbanne, France
| | - Maxime Ducret
- Hospices Civils de Lyon, Service d'Odontologie, Lyon, France.,Université de Lyon, Université Claude Bernard Lyon 1, Faculté d'Odontologie, Lyon, France.,Laboratoire de Biologie Tissulaire et Ingénierie thérapeutique, UMR 5305, CNRS, Université, UMS, Claude Bernard Lyon 1, 3444 BioSciences Gerland-Lyon Sud, Lyon, France
| | - Brigitte Alliot-Licht
- Université de Nantes, Faculté d'Odontologie, Nantes, France.,CHU de Nantes, Odontologie Conservatrice et Pédiatrique, Service d, Nantes, France
| | - Mourad Bekhouche
- Université de Lyon, Université Claude Bernard Lyon 1, Faculté d'Odontologie, Lyon, France.,Laboratoire de Biologie Tissulaire et Ingénierie thérapeutique, UMR 5305, CNRS, Université, UMS, Claude Bernard Lyon 1, 3444 BioSciences Gerland-Lyon Sud, Lyon, France
| | - Stéphanie Gobert
- Laboratoire de Biologie Tissulaire et Ingénierie thérapeutique, UMR 5305, CNRS, Université, UMS, Claude Bernard Lyon 1, 3444 BioSciences Gerland-Lyon Sud, Lyon, France
| | - Jean-Christophe Farges
- Hospices Civils de Lyon, Service d'Odontologie, Lyon, France.,Université de Lyon, Université Claude Bernard Lyon 1, Faculté d'Odontologie, Lyon, France.,Laboratoire de Biologie Tissulaire et Ingénierie thérapeutique, UMR 5305, CNRS, Université, UMS, Claude Bernard Lyon 1, 3444 BioSciences Gerland-Lyon Sud, Lyon, France
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4
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Uzozie AC, Tsui J, Lange PF. HUNTER: Sensitive Automated Characterization of Proteolytic Systems by N Termini Enrichment from Microscale Specimen. Methods Mol Biol 2022; 2456:95-122. [PMID: 35612738 DOI: 10.1007/978-1-0716-2124-0_8] [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] [Indexed: 06/15/2023]
Abstract
Proteolysis occurs at low frequency in the cellular environment. Protein N termini reveal essential mechanisms associated with cellular functions, and are useful indicators to track dysfunctional regulation of proteins and pathways in diseases. N terminomics has so far relied on labor-intensive methods, which require relatively large starting sample amounts rendering it ill-suited for high-throughput systems biology studies. Here, we describe protocols for the first scalable and automatable method for sensitive enrichment and identification of N termini from minute samples.
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Affiliation(s)
- Anuli C Uzozie
- Department of Pathology, University of British Columbia, Vancouver, BC, Canada
- Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital, Vancouver, BC, Canada
| | - Janice Tsui
- Department of Pathology, University of British Columbia, Vancouver, BC, Canada
- Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital, Vancouver, BC, Canada
| | - Philipp F Lange
- Department of Pathology, University of British Columbia, Vancouver, BC, Canada.
- Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital, Vancouver, BC, Canada.
- Department of Molecular Oncology, BC Cancer, Vancouver, BC, Canada.
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5
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Martiáñez-Vendrell X, Kikkert M. Proteomics approaches for the identification of protease substrates during virus infection. Adv Virus Res 2021; 109:135-161. [PMID: 33934826 DOI: 10.1016/bs.aivir.2021.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Proteases precisely and irreversibly catalyze the hydrolysis of peptide bonds, regulating the fate, localization, and activity of many proteins. Consequently, proteolytic activity plays an important role in fundamental cellular processes such as differentiation and migration, immunological and inflammatory reactions, apoptosis and survival. During virus infection, host proteases are involved in several processes, from cell entry to initiation, progression and resolution of inflammation. On the other hand, many viruses encode their own highly specific proteases, responsible for the proteolytic processing of viral proteins, but, at the same time, to cleave host proteins to corrupt antiviral host responses and adjust protein activity to favor viral replication. Traditionally, protease substrate identification has been addressed by means of hypothesis-driven approaches, but recent advances in proteomics have made a toolkit available to uncover the extensive repertoire of host proteins cleaved during infection, either by viral or host proteases. Here, we review the currently available proteomics-based methods that can and have contributed to the systematic and unbiased identification of new protease substrates in the context of virus-host interactions. The role of specific proteases during the course of virus infections will also be highlighted.
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Affiliation(s)
- Xavier Martiáñez-Vendrell
- Molecular Virology Laboratory, Department of Medical Microbiology, LUMC Center for Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, The Netherlands
| | - Marjolein Kikkert
- Molecular Virology Laboratory, Department of Medical Microbiology, LUMC Center for Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, The Netherlands.
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6
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Abstract
Proteases play a central role in regulating renal pathophysiology and are increasingly evaluated as actionable drug targets. Here, we review the role of proteolytic systems in inflammatory kidney disease. Inflammatory kidney diseases are associated with broad dysregulations of extracellular and intracellular proteolysis. As an example of a proteolytic system, the complement system plays a significant role in glomerular inflammatory kidney disease and is currently under clinical investigation. Based on two glomerular kidney diseases, lupus nephritis, and membranous nephropathy, we portrait two proteolytic pathomechanisms and the role of the complement system. We discuss how profiling proteolytic activity in patient samples could be used to stratify patients for more targeted interventions in inflammatory kidney diseases. We also describe novel comprehensive, quantitative tools to investigate the entirety of proteolytic processes in a tissue sample. Emphasis is placed on mass spectrometric approaches that enable the comprehensive analysis of the complement system, as well as protease activities and regulation in general.
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7
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Uzozie AC, Ergin EK, Rolf N, Tsui J, Lorentzian A, Weng SSH, Nierves L, Smith TG, Lim CJ, Maxwell CA, Reid GSD, Lange PF. PDX models reflect the proteome landscape of pediatric acute lymphoblastic leukemia but divert in select pathways. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2021; 40:96. [PMID: 33722259 PMCID: PMC7958471 DOI: 10.1186/s13046-021-01835-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 01/10/2021] [Indexed: 12/22/2022]
Abstract
Background Murine xenografts of pediatric leukemia accurately recapitulate genomic aberrations. How this translates to the functional capacity of cells remains unclear. Here, we studied global protein abundance, phosphorylation, and protein maturation by proteolytic processing in 11 pediatric B- and T- cell ALL patients and 19 corresponding xenografts. Methods Xenograft models were generated for each pediatric patient leukemia. Mass spectrometry-based methods were used to investigate global protein abundance, protein phosphorylation, and limited proteolysis in paired patient and xenografted pediatric acute B- and T- cell lymphocytic leukemia, as well as in pediatric leukemia cell lines. Targeted next-generation sequencing was utilized to examine genetic abnormalities in patients and in corresponding xenografts. Bioinformatic and statistical analysis were performed to identify functional mechanisms associated with proteins and protein post-translational modifications. Results Overall, we found xenograft proteomes to be most equivalent with their patient of origin. Protein level differences that stratified disease subtypes at diagnostic and relapse stages were largely recapitulated in xenografts. As expected, PDXs lacked multiple human leukocyte antigens and complement proteins. We found increased expression of cell cycle proteins indicating a high proliferative capacity of xenografted cells. Structural genomic changes and mutations were reflected at the protein level in patients. In contrast, the post-translational modification landscape was shaped by leukemia type and host and only to a limited degree by the patient of origin. Of 201 known pediatric oncogenic drivers and drug-targetable proteins, the KMT2 protein family showed consistently high variability between patient and corresponding xenografts. Comprehensive N terminomics revealed deregulated proteolytic processing in leukemic cells, in particular from caspase-driven cleavages found in patient cells. Conclusion Genomic and host factors shape protein and post-translational modification landscapes differently. This study highlights select areas of diverging biology while confirming murine patient-derived xenografts as a generally accurate model system. Supplementary Information The online version contains supplementary material available at 10.1186/s13046-021-01835-8.
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Affiliation(s)
- Anuli C Uzozie
- Department of Pathology, University of British Columbia, Vancouver, BC, Canada.,Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital Research Institute, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada
| | - Enes K Ergin
- Department of Pathology, University of British Columbia, Vancouver, BC, Canada.,Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital Research Institute, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada
| | - Nina Rolf
- Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital Research Institute, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada.,Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
| | - Janice Tsui
- Department of Pathology, University of British Columbia, Vancouver, BC, Canada.,Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital Research Institute, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada
| | - Amanda Lorentzian
- Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital Research Institute, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada.,Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
| | - Samuel S H Weng
- Department of Pathology, University of British Columbia, Vancouver, BC, Canada
| | - Lorenz Nierves
- Department of Pathology, University of British Columbia, Vancouver, BC, Canada.,Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital Research Institute, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada
| | - Theodore G Smith
- Department of Pathology, University of British Columbia, Vancouver, BC, Canada.,Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital Research Institute, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada
| | - C James Lim
- Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital Research Institute, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada.,Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
| | - Christopher A Maxwell
- Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital Research Institute, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada.,Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
| | - Gregor S D Reid
- Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital Research Institute, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada.,Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
| | - Philipp F Lange
- Department of Pathology, University of British Columbia, Vancouver, BC, Canada. .,Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital Research Institute, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada. .,Department of Molecular Oncology, BC Cancer Research Centre, Vancouver, BC, Canada.
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8
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Chen L, Shan Y, Yang C, Sui Z, Zhang X, Zhang L, Zhang Y. Carboxypeptidase B-Assisted Charge-Based Fractional Diagonal Chromatography for Deep Screening of C-Terminome. Anal Chem 2020; 92:8005-8009. [DOI: 10.1021/acs.analchem.0c00762] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Lingfan Chen
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Fujian Province New Drug Safety Evaluation Centre, Fujian Medical University, Fuzhou 350108, China
| | - Yichu Shan
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Chao Yang
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Zhigang Sui
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Xiaodan Zhang
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Lihua Zhang
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Yukui Zhang
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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9
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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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10
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Weng SSH, Demir F, Ergin EK, Dirnberger S, Uzozie A, Tuscher D, Nierves L, Tsui J, Huesgen PF, Lange PF. Sensitive Determination of Proteolytic Proteoforms in Limited Microscale Proteome Samples. Mol Cell Proteomics 2019; 18:2335-2347. [PMID: 31471496 PMCID: PMC6823850 DOI: 10.1074/mcp.tir119.001560] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 08/09/2019] [Indexed: 12/15/2022] Open
Abstract
Protein N termini unambiguously identify truncated, alternatively translated or modified proteoforms with distinct functions and reveal perturbations in disease. Selective enrichment of N-terminal peptides is necessary to achieve proteome-wide coverage for unbiased identification of site-specific regulatory proteolytic processing and protease substrates. However, many proteolytic processes are strictly confined in time and space and therefore can only be analyzed in minute samples that provide insufficient starting material for current enrichment protocols. Here we present High-efficiency Undecanal-based N Termini EnRichment (HUNTER), a robust, sensitive and scalable method for the analysis of previously inaccessible microscale samples. HUNTER achieved identification of >1000 N termini from as little as 2 μg raw HeLa cell lysate. Broad applicability is demonstrated by the first N-terminome analysis of sorted human primary immune cells and enriched mitochondrial fractions from pediatric cancer patients, as well as protease substrate identification from individual Arabidopsis thaliana wild type and Vacuolar Processing Enzyme-deficient mutant seedlings. We further implemented the workflow on a liquid handling system and demonstrate the feasibility of clinical degradomics by automated processing of liquid biopsies from pediatric cancer patients.
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Affiliation(s)
- Samuel S H Weng
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada; Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital, Vancouver, Canada
| | - Fatih Demir
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Germany
| | - Enes K Ergin
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada; Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital, Vancouver, Canada
| | - Sabrina Dirnberger
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Germany
| | - Anuli Uzozie
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada; Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital, Vancouver, Canada
| | - Domenic Tuscher
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Germany
| | - Lorenz Nierves
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada; Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital, Vancouver, Canada
| | - Janice Tsui
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada; Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital, Vancouver, Canada
| | - Pitter F Huesgen
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases, Medical Faculty and University Hospital, University of Cologne, Cologne, Germany.
| | - Philipp F Lange
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada; Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital, Vancouver, Canada.
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11
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Grozdanić M, Vidmar R, Vizovišek M, Fonović M. Degradomics in Biomarker Discovery. Proteomics Clin Appl 2019; 13:e1800138. [PMID: 31291060 DOI: 10.1002/prca.201800138] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Revised: 05/01/2019] [Indexed: 12/13/2022]
Abstract
The upregulation of protease expression and proteolytic activity is implicated in numerous pathological conditions such as neurodegeneration, cancer, cardiovascular and autoimmune diseases, and bone degeneration. During disease progression, various proteases form characteristic patterns of cleaved proteins and peptides, which can affect disease severity and course of progression. It has been shown that qualitative and quantitative monitoring of cleaved protease substrates can provide relevant prognostic, diagnostic, and therapeutic information. As proteolytic fragments and peptides generated in the affected tissue are commonly translocated to blood, urine, and other proximal fluids, their possible application as biomarkers is the subject of ongoing research. The field of degradomics has been established to enable the global identification of proteolytic events on the organism level, utilizing proteomic approaches and sample preparation techniques that facilitate the detection of proteolytic processing of protease substrates in complex biological samples. In this review, some of the latest developments in degradomic methodologies used for the identification and validation of biologically relevant proteolytic events and their application in the search for clinically relevant biomarker candidates are presented. The current state of degradomics in clinics is discussed and the future perspectives of the field are outlined.
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Affiliation(s)
- Marija Grozdanić
- Department of Biochemistry, Molecular and Structural Biology, Jozef Stefan Institute, SI-1000, Ljubljana, Slovenia.,International Postgraduate School Jožef Stefan, SI-1000, Ljubljana, Slovenia
| | - Robert Vidmar
- Department of Biochemistry, Molecular and Structural Biology, Jozef Stefan Institute, SI-1000, Ljubljana, Slovenia
| | - Matej Vizovišek
- Department of Biochemistry, Molecular and Structural Biology, Jozef Stefan Institute, SI-1000, Ljubljana, Slovenia
| | - Marko Fonović
- Department of Biochemistry, Molecular and Structural Biology, Jozef Stefan Institute, SI-1000, Ljubljana, Slovenia
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12
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Perrar A, Dissmeyer N, Huesgen PF. New beginnings and new ends: methods for large-scale characterization of protein termini and their use in plant biology. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:2021-2038. [PMID: 30838411 PMCID: PMC6460961 DOI: 10.1093/jxb/erz104] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 02/27/2019] [Indexed: 05/17/2023]
Abstract
Dynamic regulation of protein function and abundance plays an important role in virtually every aspect of plant life. Diversifying mechanisms at the RNA and protein level result in many protein molecules with distinct sequence and modification, termed proteoforms, arising from a single gene. Distinct protein termini define proteoforms arising from translation of alternative transcripts, use of alternative translation initiation sites, and different co- and post-translational modifications of the protein termini. Also site-specific proteolytic processing by endo- and exoproteases generates truncated proteoforms, defined by distinct protease-generated neo-N- and neo-C-termini, that may exhibit altered activity, function, and localization compared with their precursor proteins. In eukaryotes, the N-degron pathway targets cytosolic proteins, exposing destabilizing N-terminal amino acids and/or destabilizing N-terminal modifications for proteasomal degradation. This enables rapid and selective removal not only of unfolded proteins, but also of substrate proteoforms generated by proteolytic processing or changes in N-terminal modifications. Here we summarize current protocols enabling proteome-wide analysis of protein termini, which have provided important new insights into N-terminal modifications and protein stability determinants, protein maturation pathways, and protease-substrate relationships in plants.
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Affiliation(s)
- Andreas Perrar
- Forschungszentrum Jülich, Central Institute for Engineering, Electronics and Analytics, ZEA-3 Analytics, Jülich, Germany
| | - Nico Dissmeyer
- Independent Junior Research Group on Protein Recognition and Degradation, Leibniz Institute of Plant Biochemistry (IPB), Weinberg, Halle (Saale), Germany
- ScienceCampus Halle – Plant-based Bioeconomy, Halle (Saale), Germany
| | - Pitter F Huesgen
- Forschungszentrum Jülich, Central Institute for Engineering, Electronics and Analytics, ZEA-3 Analytics, Jülich, Germany
- Medical Faculty and University Hospital, University of Cologne, Cologne, Germany
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13
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Lorentzian A, Uzozie A, Lange PF. Origins and clinical relevance of proteoforms in pediatric malignancies. Expert Rev Proteomics 2019; 16:185-200. [PMID: 30700156 DOI: 10.1080/14789450.2019.1575206] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
INTRODUCTION Cancer changes the proteome in complex ways that reach well beyond simple changes in protein abundance. Genomic and transcriptional variations and post-translational protein modification create functional variants of a protein, known as proteoforms. Childhood cancers have fewer genomic alterations but show equally dramatic phenotypic changes as malignant cells in adults. Therefore, unraveling the complexities of the proteome is even more important in pediatric malignancies. Areas covered: In this review, the biological origins of proteoforms and technological advancements in the study of proteoforms are discussed. Particular emphasis is given to their implication in childhood malignancies and the critical role of cancer-specific proteoforms for the next generation of cancer therapies and diagnostics. Expert opinion: Recent advancements in technology have led to a better understanding of the underlying mechanisms of tumorigenesis. This has been critical for the development of more effective and less harmful treatments that are based on direct targeting of altered proteins and deregulated pathways. As proteome coverage and the ability to detect complex proteoforms increase, the most need for change is in data compilation and database availability to mediate high-level data analysis and allow for better functional annotation of proteoforms.
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Affiliation(s)
- Amanda Lorentzian
- a Department of Cell and Developmental Biology , University of British Columbia , Vancouver , BC , Canada.,b Michael Cuccione Childhood Cancer Research Program , BC Children's Hospital Research Institute , Vancouver , BC , Canada
| | - Anuli Uzozie
- b Michael Cuccione Childhood Cancer Research Program , BC Children's Hospital Research Institute , Vancouver , BC , Canada.,c Department of Pathology and Laboratory Medicine , University of British Columbia , Vancouver , BC , Canada
| | - Philipp F Lange
- a Department of Cell and Developmental Biology , University of British Columbia , Vancouver , BC , Canada.,b Michael Cuccione Childhood Cancer Research Program , BC Children's Hospital Research Institute , Vancouver , BC , Canada.,c Department of Pathology and Laboratory Medicine , University of British Columbia , Vancouver , BC , Canada
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14
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Abstract
Proteases drive the life cycle of all proteins, ensuring the transportation and activation of newly minted, would-be proteins into their functional form while recycling spent or unneeded proteins. Far from their image as engines of protein digestion, proteases play fundamental roles in basic physiology and regulation at multiple levels of systems biology. Proteases are intimately associated with disease and modulation of proteolytic activity is the presumed target for successful therapeutics. "Proteases: Pivot Points in Functional Proteomics" examines the crucial roles of proteolysis across a wide range of physiological processes and diseases. The existing and potential impacts of proteolysis-related activity on drug and biomarker development are presented in detail. All told the decisive roles of proteases in four major categories comprising 23 separate subcategories are addressed. Within this construct, 15 sets of subject-specific, tabulated data are presented that include identification of proteases, protease inhibitors, substrates, and their actions. Said data are derived from and confirmed by over 300 references. Cross comparison of datasets indicates that proteases, their inhibitors/promoters and substrates intersect over a range of physiological processes and diseases, both chronic and pathogenic. Indeed, "Proteases: Pivot Points …" closes by dramatizing this very point through association of (pro)Thrombin and Fibrin(ogen) with: hemostasis, innate immunity, cardiovascular and metabolic disease, cancer, neurodegeneration, and bacterial self-defense.
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Affiliation(s)
- Ingrid M Verhamme
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, USA.
| | - Sarah E Leonard
- Chemical and Biomolecular Engineering, University of Illinois Champaign-Urbana School of Chemical Sciences, Champaign, IL, USA
| | - Ray C Perkins
- New Liberty Proteomics Corporation, New Liberty, KY, USA.
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15
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Späth MR, Bartram MP, Palacio-Escat N, Hoyer KJR, Debes C, Demir F, Schroeter CB, Mandel AM, Grundmann F, Ciarimboli G, Beyer A, Kizhakkedathu JN, Brodesser S, Göbel H, Becker JU, Benzing T, Schermer B, Höhne M, Burst V, Saez-Rodriguez J, Huesgen PF, Müller RU, Rinschen MM. The proteome microenvironment determines the protective effect of preconditioning in cisplatin-induced acute kidney injury. Kidney Int 2018; 95:333-349. [PMID: 30522767 DOI: 10.1016/j.kint.2018.08.037] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 07/24/2018] [Accepted: 08/16/2018] [Indexed: 01/18/2023]
Abstract
Acute kidney injury (AKI) leads to significant morbidity and mortality; unfortunately, strategies to prevent or treat AKI are lacking. In recent years, several preconditioning protocols have been shown to be effective in inducing organ protection in rodent models. Here, we characterized two of these interventions-caloric restriction and hypoxic preconditioning-in a mouse model of cisplatin-induced AKI and investigated the underlying mechanisms by acquisition of multi-layered omic data (transcriptome, proteome, N-degradome) and functional parameters in the same animals. Both preconditioning protocols markedly ameliorated cisplatin-induced loss of kidney function, and caloric restriction also induced lipid synthesis. Bioinformatic analysis revealed mRNA-independent proteome alterations affecting the extracellular space, mitochondria, and transporters. Interestingly, our analyses revealed a strong dissociation of protein and RNA expression after cisplatin treatment that showed a strong correlation with the degree of damage. N-degradomic analysis revealed that most posttranscriptional changes were determined by arginine-specific proteolytic processing. This included a characteristic cisplatin-activated complement signature that was prevented by preconditioning. Amyloid and acute-phase proteins within the cortical parenchyma showed a similar response. Extensive analysis of disease-associated molecular patterns suggested that transcription-independent deposition of amyloid P-component serum protein may be a key component in the microenvironmental contribution to kidney damage. This proof-of-principle study provides new insights into the pathogenesis of cisplatin-induced AKI and the molecular mechanisms underlying organ protection by correlating phenotypic and multi-layered omics data.
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Affiliation(s)
- Martin R Späth
- Department II of Internal Medicine, University of Cologne, Cologne, Germany; Center for Molecular Medicine, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Malte P Bartram
- Department II of Internal Medicine, University of Cologne, Cologne, Germany; Center for Molecular Medicine, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Nicolàs Palacio-Escat
- COMBINE-Joint Research Center for Computational Biomedicine RWTH Aachen University, Aachen, Germany
| | - K Johanna R Hoyer
- Department II of Internal Medicine, University of Cologne, Cologne, Germany; Center for Molecular Medicine, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Cedric Debes
- Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany; Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany
| | - Fatih Demir
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Jülich, Germany
| | - Christina B Schroeter
- Department II of Internal Medicine, University of Cologne, Cologne, Germany; Center for Molecular Medicine, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Amrei M Mandel
- Department II of Internal Medicine, University of Cologne, Cologne, Germany; Center for Molecular Medicine, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Franziska Grundmann
- Department II of Internal Medicine, University of Cologne, Cologne, Germany; Center for Molecular Medicine, University of Cologne, Cologne, Germany
| | - Giuliano Ciarimboli
- Department of Experimental Nephrology, University Hospital of Münster, Münster, Germany
| | - Andreas Beyer
- Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany; Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany
| | - Jayachandran N Kizhakkedathu
- Department of Pathology, Centre for Blood Research, The University of British Columbia, British Columbia, Vancouver, Canada; Laboratory Medicine, Department of Chemistry, The University of British Columbia, British Columbia, Vancouver, Canada
| | - Susanne Brodesser
- Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Heike Göbel
- Institute of Pathology, University Hospital of Cologne, Cologne, Germany
| | - Jan U Becker
- Institute of Pathology, University Hospital of Cologne, Cologne, Germany
| | - Thomas Benzing
- Department II of Internal Medicine, University of Cologne, Cologne, Germany; Center for Molecular Medicine, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany; Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany
| | - Bernhard Schermer
- Department II of Internal Medicine, University of Cologne, Cologne, Germany; Center for Molecular Medicine, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany; Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany
| | - Martin Höhne
- Department II of Internal Medicine, University of Cologne, Cologne, Germany; Center for Molecular Medicine, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany; Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany
| | - Volker Burst
- Department II of Internal Medicine, University of Cologne, Cologne, Germany; Center for Molecular Medicine, University of Cologne, Cologne, Germany
| | - Julio Saez-Rodriguez
- COMBINE-Joint Research Center for Computational Biomedicine RWTH Aachen University, Aachen, Germany; Faculty of Medicine Bioquant, Institute for Computational Biomedicine, Heidelberg University, Heidelberg, Germany
| | - Pitter F Huesgen
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Jülich, Germany
| | - Roman-Ulrich Müller
- Department II of Internal Medicine, University of Cologne, Cologne, Germany; Center for Molecular Medicine, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany; Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany.
| | - Markus M Rinschen
- Department II of Internal Medicine, University of Cologne, Cologne, Germany; Center for Molecular Medicine, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany; Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany.
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16
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Herrera C, Escalante T, Rucavado A, Fox JW, Gutiérrez JM. Metalloproteinases in disease: identification of biomarkers of tissue damage through proteomics. Expert Rev Proteomics 2018; 15:967-982. [DOI: 10.1080/14789450.2018.1538800] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Cristina Herrera
- Facultad de Farmacia, Universidad de Costa Rica, San José, Costa Rica
| | - Teresa Escalante
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Alexandra Rucavado
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Jay W. Fox
- School of Medicine, University of Virginia, Charlottesville, VA22959, USA
| | - José María Gutiérrez
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
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17
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Rinschen MM, Huesgen PF, Koch RE. The podocyte protease web: uncovering the gatekeepers of glomerular disease. Am J Physiol Renal Physiol 2018; 315:F1812-F1816. [PMID: 30230368 DOI: 10.1152/ajprenal.00380.2018] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Proteases regulate glomerular physiology. The last decade has revealed a multitude of podocyte proteases that govern the glomerular response to numerous chemical, mechanical, and metabolic cues. These proteases form a protein signaling web that integrates stress stimuli and serves as a key controller of the glomerular microenvironment. Both the extracellular and intracellular proteolytic networks are perturbed in focal segmental glomerulosclerosis, as well as hypertensive and diabetic nephropathy. Accordingly, the highly intertwined podocyte protease web is an integrative part of the podocyte's damage response. Novel mass spectrometry-based technologies will help to untangle this proteolytic network: functional readouts acquired from deep podocyte proteomics, single glomerular proteomics, and degradomics have exposed unanticipated protease activity in podocytes. Future efforts should characterize the interdependency and upstream regulation of key proteases, along with their role in promoting tissue heterogeneity in glomerular diseases. These efforts will not only illuminate the machinery of podocyte proteostasis but also reveal avenues for therapeutic intervention in the podocyte protease web.
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Affiliation(s)
- Markus M Rinschen
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne , Cologne , Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne , Cologne , Germany.,Center for Mass Spectrometry and Metabolomics, The Scripps Research Institute , La Jolla, California
| | - Pitter F Huesgen
- Central Institute for Engineering, Electronics and Analytics ZEA-3, Forschungszentrum Jülich, Jülich , Germany
| | - Rachelle E Koch
- Division of Graduate Medical Sciences, Boston University School of Medicine , Boston, Massachusetts
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18
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Savickas S, Auf dem Keller U. Targeted degradomics in protein terminomics and protease substrate discovery. Biol Chem 2017; 399:47-54. [PMID: 28850541 DOI: 10.1515/hsz-2017-0187] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 08/21/2017] [Indexed: 02/06/2023]
Abstract
Targeted degradomics integrates positional information into mass spectrometry (MS)-based targeted proteomics workflows and thereby enables analysis of proteolytic cleavage events with unprecedented specificity and sensitivity. Rapid progress in the establishment of protease-substrate relations provides extensive degradomics target lists that now can be tested with help of selected and parallel reaction monitoring (S/PRM) in complex biological systems, where proteases act in physiological environments. In this minireview, we describe the general principles of targeted degradomics, outline the generic experimental workflow of the methodology and highlight recent and future applications in protease research.
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Affiliation(s)
- Simonas Savickas
- Institute of Molecular Health Sciences, ETH Zurich, Otto-Stern-Weg 7, CH-8093 Zurich, Switzerland
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Anker Engelunds Vej, Building 301, DK-2800 Kgs. Lyngby, Denmark
| | - Ulrich Auf dem Keller
- Institute of Molecular Health Sciences, ETH Zurich, Otto-Stern-Weg 7, CH-8093 Zurich, Switzerland
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Anker Engelunds Vej, Building 301, DK-2800 Kgs. Lyngby, Denmark
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19
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Rinschen MM, Hoppe AK, Grahammer F, Kann M, Völker LA, Schurek EM, Binz J, Höhne M, Demir F, Malisic M, Huber TB, Kurschat C, Kizhakkedathu JN, Schermer B, Huesgen PF, Benzing T. N-Degradomic Analysis Reveals a Proteolytic Network Processing the Podocyte Cytoskeleton. J Am Soc Nephrol 2017; 28:2867-2878. [PMID: 28724775 DOI: 10.1681/asn.2016101119] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 05/08/2017] [Indexed: 11/03/2022] Open
Abstract
Regulated intracellular proteostasis, controlled in part by proteolysis, is essential in maintaining the integrity of podocytes and the glomerular filtration barrier of the kidney. We applied a novel proteomics technology that enables proteome-wide identification, mapping, and quantification of protein N-termini to comprehensively characterize cleaved podocyte proteins in the glomerulus in vivo We found evidence that defined proteolytic cleavage results in various proteoforms of important podocyte proteins, including those of podocin, nephrin, neph1, α-actinin-4, and vimentin. Quantitative mapping of N-termini demonstrated perturbation of protease action during podocyte injury in vitro, including diminished proteolysis of α-actinin-4. Differentially regulated protease substrates comprised cytoskeletal proteins as well as intermediate filaments. Determination of preferential protease motifs during podocyte damage indicated activation of caspase proteases and inhibition of arginine-specific proteases. Several proteolytic processes were clearly site-specific, were conserved across species, and could be confirmed by differential migration behavior of protein fragments in gel electrophoresis. Some of the proteolytic changes discovered in vitro also occurred in two in vivo models of podocyte damage (WT1 heterozygous knockout mice and puromycin aminonucleoside-treated rats). Thus, we provide direct and systems-level evidence that the slit diaphragm and podocyte cytoskeleton are regulated targets of proteolytic modification, which is altered upon podocyte damage.
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Affiliation(s)
- Markus M Rinschen
- Department II of Internal Medicine.,Center for Molecular Medicine Cologne (CMMC).,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), and.,Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany
| | - Ann-Kathrin Hoppe
- Department II of Internal Medicine.,Center for Molecular Medicine Cologne (CMMC)
| | - Florian Grahammer
- Department of Medicine III, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Department of Medicine IV, Medical Center and Faculty of Medicine - University of Freiburg, Freiburg, Germany
| | - Martin Kann
- Department II of Internal Medicine.,Center for Molecular Medicine Cologne (CMMC)
| | - Linus A Völker
- Department II of Internal Medicine.,Center for Molecular Medicine Cologne (CMMC)
| | - Eva-Maria Schurek
- Department II of Internal Medicine.,Center for Molecular Medicine Cologne (CMMC)
| | - Julie Binz
- Department II of Internal Medicine.,Center for Molecular Medicine Cologne (CMMC)
| | - Martin Höhne
- Department II of Internal Medicine.,Center for Molecular Medicine Cologne (CMMC).,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), and.,Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany
| | - Fatih Demir
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Jülich, Germany
| | - Milena Malisic
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Jülich, Germany
| | - Tobias B Huber
- Department of Medicine III, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Department of Medicine IV, Medical Center and Faculty of Medicine - University of Freiburg, Freiburg, Germany.,BIOSS Centre for Biological Signalling Studies and Center for Biological Systems Analysis (ZBSA), Albert-Ludwigs-University, Freiburg, Germany; and
| | - Christine Kurschat
- Department II of Internal Medicine.,Center for Molecular Medicine Cologne (CMMC)
| | - Jayachandran N Kizhakkedathu
- Centre for Blood Research, Department of Pathology and Laboratory Medicine, Department of Chemistry, University of British Columbia, Vancouver, Canada
| | - Bernhard Schermer
- Department II of Internal Medicine.,Center for Molecular Medicine Cologne (CMMC).,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), and.,Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany
| | - Pitter F Huesgen
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Jülich, Germany;
| | - Thomas Benzing
- Department II of Internal Medicine, .,Center for Molecular Medicine Cologne (CMMC).,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), and.,Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany
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20
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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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21
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22
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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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23
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24
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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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Lange PF, Huesgen PF, Nguyen K, Overall CM. Annotating N termini for the human proteome project: N termini and Nα-acetylation status differentiate stable cleaved protein species from degradation remnants in the human erythrocyte proteome. J Proteome Res 2014; 13:2028-44. [PMID: 24555563 PMCID: PMC3979129 DOI: 10.1021/pr401191w] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A goal of the Chromosome-centric Human Proteome Project is to identify all human protein species. With 3844 proteins annotated as "missing", this is challenging. Moreover, proteolytic processing generates new protein species with characteristic neo-N termini that are frequently accompanied by altered half-lives, function, interactions, and location. Enucleated and largely void of internal membranes and organelles, erythrocytes are simple yet proteomically challenging cells due to the high hemoglobin content and wide dynamic range of protein concentrations that impedes protein identification. Using the N-terminomics procedure TAILS, we identified 1369 human erythrocyte natural and neo-N-termini and 1234 proteins. Multiple semitryptic N-terminal peptides exhibited improved mass spectrometric identification properties versus the intact tryptic peptide enabling identification of 281 novel erythrocyte proteins and six missing proteins identified for the first time in the human proteome. With an improved bioinformatics workflow, we developed a new classification system and the Terminus Cluster Score. Thereby we described a new stabilizing N-end rule for processed protein termini, which discriminates novel protein species from degradation remnants, and identified protein domain hot spots susceptible to cleavage. Strikingly, 68% of the N-termini were within genome-encoded protein sequences, revealing alternative translation initiation sites, pervasive endoproteolytic processing, and stabilization of protein fragments in vivo. The mass spectrometry proteomics data have been deposited to ProteomeXchange with the data set identifier <PXD000434>.
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Affiliation(s)
- Philipp F Lange
- Centre for Blood Research, University of British Columbia , 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada
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