1
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Behera RN, Bisht VS, Giri K, Ambatipudi K. Realm of proteomics in breast cancer management and drug repurposing to alleviate intricacies of treatment. Proteomics Clin Appl 2023; 17:e2300016. [PMID: 37259687 DOI: 10.1002/prca.202300016] [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: 02/16/2023] [Revised: 05/10/2023] [Accepted: 05/15/2023] [Indexed: 06/02/2023]
Abstract
Breast cancer, a multi-networking heterogeneous disease, has emerged as a serious impediment to progress in clinical oncology. Although technological advancements and emerging cancer research studies have mitigated breast cancer lethality, a precision cancer-oriented solution has not been achieved. Thus, this review will persuade the acquiescence of proteomics-based diagnostic and therapeutic options in breast cancer management. Recently, the evidence of breast cancer health surveillance through imaging proteomics, single-cell proteomics, interactomics, and post-translational modification (PTM) tracking, to construct proteome maps and proteotyping for stage-specific and sample-specific cancer subtyping have outperformed conventional ways of dealing with breast cancer by increasing diagnostic efficiency, prognostic value, and predictive response. Additionally, the paradigm shift in applied proteomics for designing a chemotherapy regimen to identify novel drug targets with minor adverse effects has been elaborated. Finally, the potential of proteomics in alleviating the occurrence of chemoresistance and enhancing reprofiled drugs' effectiveness to combat therapeutic obstacles has been discussed. Owing to the enormous potential of proteomics techniques, the clinical recognition of proteomics in breast cancer management can be achievable and therapeutic intricacies can be surmountable.
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Affiliation(s)
- Rama N Behera
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Vinod S Bisht
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Kuldeep Giri
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Kiran Ambatipudi
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
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2
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Lu C, Lubin JH, Sarma VV, Stentz SZ, Wang G, Wang S, Khare SD. Prediction and design of protease enzyme specificity using a structure-aware graph convolutional network. Proc Natl Acad Sci U S A 2023; 120:e2303590120. [PMID: 37729196 PMCID: PMC10523478 DOI: 10.1073/pnas.2303590120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 08/14/2023] [Indexed: 09/22/2023] Open
Abstract
Site-specific proteolysis by the enzymatic cleavage of small linear sequence motifs is a key posttranslational modification involved in physiology and disease. The ability to robustly and rapidly predict protease-substrate specificity would also enable targeted proteolytic cleavage by designed proteases. Current methods for predicting protease specificity are limited to sequence pattern recognition in experimentally derived cleavage data obtained for libraries of potential substrates and generated separately for each protease variant. We reasoned that a more semantically rich and robust model of protease specificity could be developed by incorporating the energetics of molecular interactions between protease and substrates into machine learning workflows. We present Protein Graph Convolutional Network (PGCN), which develops a physically grounded, structure-based molecular interaction graph representation that describes molecular topology and interaction energetics to predict enzyme specificity. We show that PGCN accurately predicts the specificity landscapes of several variants of two model proteases. Node and edge ablation tests identified key graph elements for specificity prediction, some of which are consistent with known biochemical constraints for protease:substrate recognition. We used a pretrained PGCN model to guide the design of protease libraries for cleaving two noncanonical substrates, and found good agreement with experimental cleavage results. Importantly, the model can accurately assess designs featuring diversity at positions not present in the training data. The described methodology should enable the structure-based prediction of specificity landscapes of a wide variety of proteases and the construction of tailor-made protease editors for site-selectively and irreversibly modifying chosen target proteins.
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Affiliation(s)
- Changpeng Lu
- Institute for Quantitative Biomedicine, Rutgers–The State University of New Jersey, Piscataway, NJ08854
| | - Joseph H. Lubin
- Department of Chemistry and Chemical Biology, Rutgers–The State University of New Jersey, Piscataway, NJ08854
| | - Vidur V. Sarma
- Institute for Quantitative Biomedicine, Rutgers–The State University of New Jersey, Piscataway, NJ08854
| | | | - Guanyang Wang
- Department of Statistics, Rutgers–The State University of New Jersey, Piscataway, NJ08854
| | - Sijian Wang
- Institute for Quantitative Biomedicine, Rutgers–The State University of New Jersey, Piscataway, NJ08854
- Department of Statistics, Rutgers–The State University of New Jersey, Piscataway, NJ08854
| | - Sagar D. Khare
- Institute for Quantitative Biomedicine, Rutgers–The State University of New Jersey, Piscataway, NJ08854
- Department of Chemistry and Chemical Biology, Rutgers–The State University of New Jersey, Piscataway, NJ08854
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3
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Shahvali S, Rahiman N, Jaafari MR, Arabi L. Targeting fibroblast activation protein (FAP): advances in CAR-T cell, antibody, and vaccine in cancer immunotherapy. Drug Deliv Transl Res 2023; 13:2041-2056. [PMID: 36840906 DOI: 10.1007/s13346-023-01308-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/01/2023] [Indexed: 02/26/2023]
Abstract
Fibroblast activation protein (FAP) is a serine protease with dual enzymatic activities overexpressed in cancer-associated fibroblasts (CAFs) in several tumor types, while its expression in healthy adult tissues is scarce. FAP overexpression on CAFs is associated with poor prognosis and plays an important role in tumor development, progression, and invasion. Therefore, FAP is considered a robust therapeutic target for cancer therapy. Here, we try to review and highlight the recent advances in immunotherapies for FAP targeting including the anti-FAP antibodies and immunoconjugates, FAP chimeric antigen receptor (CAR)-T cell, and various FAP vaccines in a preclinical and clinical setting. Subsequently, a discussion on the challenges and prospects associated with the development and translation of effective and safe therapies for targeting and depletion of FAP is provided. We proposed that new CAR-T cell engineering strategies and nanotechnology-based systems as well as advanced functional biomaterials can be used to improve the efficiency and safety of CAR-T cells and vaccines against FAP for more personalized immunotherapy. This review emphasizes the immune targeting of FAP as an emerging stromal candidate and one of the crucial elements in immunotherapy and shows the potential for improvement of current cancer therapy. A summary of different immunotherapy approaches to target fibroblast activation protein (FAP) for cancer therapy.
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Affiliation(s)
- Sedigheh Shahvali
- Nanotechnology Research Center, Institute of Pharmaceutical Technology, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Niloufar Rahiman
- Nanotechnology Research Center, Institute of Pharmaceutical Technology, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mahmoud Reza Jaafari
- Nanotechnology Research Center, Institute of Pharmaceutical Technology, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Pharmaceutical Nanotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Leila Arabi
- Nanotechnology Research Center, Institute of Pharmaceutical Technology, Mashhad University of Medical Sciences, Mashhad, Iran.
- Department of Pharmaceutical Nanotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
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4
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Lu C, Lubin JH, Sarma VV, Stentz SZ, Wang G, Wang S, Khare SD. Prediction and Design of Protease Enzyme Specificity Using a Structure-Aware Graph Convolutional Network. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.16.528728. [PMID: 36824945 PMCID: PMC9949123 DOI: 10.1101/2023.02.16.528728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Site-specific proteolysis by the enzymatic cleavage of small linear sequence motifs is a key post-translational modification involved in physiology and disease. The ability to robustly and rapidly predict protease substrate specificity would also enable targeted proteolytic cleavage - editing - of a target protein by designed proteases. Current methods for predicting protease specificity are limited to sequence pattern recognition in experimentally-derived cleavage data obtained for libraries of potential substrates and generated separately for each protease variant. We reasoned that a more semantically rich and robust model of protease specificity could be developed by incorporating the three-dimensional structure and energetics of molecular interactions between protease and substrates into machine learning workflows. We present Protein Graph Convolutional Network (PGCN), which develops a physically-grounded, structure-based molecular interaction graph representation that describes molecular topology and interaction energetics to predict enzyme specificity. We show that PGCN accurately predicts the specificity landscapes of several variants of two model proteases: the NS3/4 protease from the Hepatitis C virus (HCV) and the Tobacco Etch Virus (TEV) proteases. Node and edge ablation tests identified key graph elements for specificity prediction, some of which are consistent with known biochemical constraints for protease:substrate recognition. We used a pre-trained PGCN model to guide the design of TEV protease libraries for cleaving two non-canonical substrates, and found good agreement with experimental cleavage results. Importantly, the model can accurately assess designs featuring diversity at positions not present in the training data. The described methodology should enable the structure-based prediction of specificity landscapes of a wide variety of proteases and the construction of tailor-made protease editors for site-selectively and irreversibly modifying chosen target proteins.
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Affiliation(s)
- Changpeng Lu
- Institute for Quantitative Biomedicine, Rutgers - The State University of New Jersey, Piscataway, NJ
| | - Joseph H. Lubin
- Department of Chemistry & Chemical Biology, Rutgers - The State University of New Jersey, Piscataway, NJ
| | - Vidur V. Sarma
- Institute for Quantitative Biomedicine, Rutgers - The State University of New Jersey, Piscataway, NJ
| | | | - Guanyang Wang
- Department of Statistics, Rutgers - The State University of New Jersey, Piscataway, NJ
| | - Sijian Wang
- Institute for Quantitative Biomedicine, Rutgers - The State University of New Jersey, Piscataway, NJ
- Department of Statistics, Rutgers - The State University of New Jersey, Piscataway, NJ
| | - Sagar D. Khare
- Institute for Quantitative Biomedicine, Rutgers - The State University of New Jersey, Piscataway, NJ
- Department of Chemistry & Chemical Biology, Rutgers - The State University of New Jersey, Piscataway, NJ
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5
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Mijanović O, Jakovleva A, Branković A, Zdravkova K, Pualic M, Belozerskaya TA, Nikitkina AI, Parodi A, Zamyatnin AA. Cathepsin K in Pathological Conditions and New Therapeutic and Diagnostic Perspectives. Int J Mol Sci 2022; 23:ijms232213762. [PMID: 36430239 PMCID: PMC9698382 DOI: 10.3390/ijms232213762] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/03/2022] [Accepted: 11/05/2022] [Indexed: 11/10/2022] Open
Abstract
Cathepsin K (CatK) is a part of the family of cysteine proteases involved in many important processes, including the degradation activity of collagen 1 and elastin in bone resorption. Changes in levels of CatK are associated with various pathological conditions, primarily related to bone and cartilage degradation, such as pycnodysostosis (associated with CatK deficiency), osteoporosis, and osteoarthritis (associated with CatK overexpression). Recently, the increased secretion of CatK is being highly correlated to vascular inflammation, hypersensitivity pneumonitis, Wegener granulomatosis, berylliosis, tuberculosis, as well as with tumor progression. Due to the wide spectrum of diseases in which CatK is involved, the design and validation of active site-specific inhibitors has been a subject of keen interest in pharmaceutical companies in recent decades. In this review, we summarized the molecular background of CatK and its involvement in various diseases, as well as its clinical significance for diagnosis and therapy.
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Affiliation(s)
- Olja Mijanović
- Dia-M, LCC, 7 b.3 Magadanskaya Str., 129345 Moscow, Russia
- The Human Pathology Department, Sechenov First Moscow State University, 119991 Moscow, Russia
| | | | - Ana Branković
- Department of Forensics Engineering, University of Criminal Investigation and Police Studies, Cara Dusana 196, 11000 Belgrade, Serbia
| | - Kristina Zdravkova
- AD Alkaloid Skopje, Boulevar Alexander the Great 12, 1000 Skopje, North Macedonia
| | - Milena Pualic
- Institute Cardiovascular Diseases Dedinje, Heroja Milana Tepica 1, 11000 Belgrade, Serbia
| | - Tatiana A. Belozerskaya
- Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia
| | - Angelina I. Nikitkina
- ArhiMed Clinique for New Medical Technologies, Vavilova St. 68/2, 119261 Moscow, Russia
| | - Alessandro Parodi
- Scientific Center for Translation Medicine, Sirius University of Science and Technology, 354340 Sochi, Russia
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - Andrey A. Zamyatnin
- Scientific Center for Translation Medicine, Sirius University of Science and Technology, 354340 Sochi, Russia
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
- Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7X, UK
- Correspondence: ; Tel.: +7-9261180220
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6
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Fang Z, Wanigasekara MSK, Yepremyan A, Lam B, Thapa P, Foss FW, Chowdhury SM. Mass Spectrometry-Cleavable Protein N-Terminal Tagging Strategy for System-Level Protease Activity Profiling. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:189-197. [PMID: 34928623 DOI: 10.1021/jasms.1c00350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Proteolysis is one of the most important protein post-translational modifications (PTMs) that influences the functions, activities, and structures of nearly all proteins during their lifetime. To facilitate the targeted identification of low-abundant proteolytic products, we devised a strategy incorporating a novel biotinylated reagent PFP (pentafluorophenyl)-Rink-biotin to specifically target, enrich and identify proteolytic N-termini. Within the PFP-Rink-biotin reagent, a mass spectrometry (MS)-cleavable feature was designed to assist in the unambiguous confirmation of the enriched proteolytic N-termini. The proof-of-concept study was performed with multiple standard proteins whose N-termini were successfully modified, enriched and identified by a signature ion (SI) in the MS/MS fragmentation, along with the determination of N-terminal peptide sequences by multistage tandem MS of the complementary fragment generated after the cleavage of MS-cleavable bond. For large-scale application, the enrichment and identification of protein N-termini from Escherichia coli cells were demonstrated, facilitated by an in-house developed NTermFinder bioinformatics workflow. We believe this approach will be beneficial in improving the confidence of identifying proteolytic substrates in a native cellular environment.
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Affiliation(s)
- Zixiang Fang
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington Texas 76019, United States
| | - Maheshika S K Wanigasekara
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington Texas 76019, United States
| | - Akop Yepremyan
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington Texas 76019, United States
| | - Brandon Lam
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington Texas 76019, United States
| | - Pawan Thapa
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington Texas 76019, United States
| | - Frank W Foss
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington Texas 76019, United States
| | - Saiful M Chowdhury
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington Texas 76019, United States
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7
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Kwon YW, Jo HS, Bae S, Seo Y, Song P, Song M, Yoon JH. Application of Proteomics in Cancer: Recent Trends and Approaches for Biomarkers Discovery. Front Med (Lausanne) 2021; 8:747333. [PMID: 34631760 PMCID: PMC8492935 DOI: 10.3389/fmed.2021.747333] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 08/26/2021] [Indexed: 12/12/2022] Open
Abstract
Proteomics has become an important field in molecular sciences, as it provides valuable information on the identity, expression levels, and modification of proteins. For example, cancer proteomics unraveled key information in mechanistic studies on tumor growth and metastasis, which has contributed to the identification of clinically applicable biomarkers as well as therapeutic targets. Several cancer proteome databases have been established and are being shared worldwide. Importantly, the integration of proteomics studies with other omics is providing extensive data related to molecular mechanisms and target modulators. These data may be analyzed and processed through bioinformatic pipelines to obtain useful information. The purpose of this review is to provide an overview of cancer proteomics and recent advances in proteomic techniques. In particular, we aim to offer insights into current proteomics studies of brain cancer, in which proteomic applications are in a relatively early stage. This review covers applications of proteomics from the discovery of biomarkers to the characterization of molecular mechanisms through advances in technology. Moreover, it addresses global trends in proteomics approaches for translational research. As a core method in translational research, the continued development of this field is expected to provide valuable information at a scale beyond that previously seen.
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Affiliation(s)
- Yang Woo Kwon
- Neurodegenerative Diseases Research Group, Korea Brain Research Institute, Daegu, South Korea
| | - Han-Seul Jo
- Neurodegenerative Diseases Research Group, Korea Brain Research Institute, Daegu, South Korea
| | - Sungwon Bae
- Neurodegenerative Diseases Research Group, Korea Brain Research Institute, Daegu, South Korea
| | - Youngsuk Seo
- Neurodegenerative Diseases Research Group, Korea Brain Research Institute, Daegu, South Korea
| | - Parkyong Song
- Department of Convergence Medicine, Pusan National University School of Medicine, Yangsan, South Korea
| | - Minseok Song
- Department of Life Sciences, Yeungnam University, Gyeongsan, South Korea
| | - Jong Hyuk Yoon
- Neurodegenerative Diseases Research Group, Korea Brain Research Institute, Daegu, South Korea
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Abstract
Significance: The vascular extracellular matrix (ECM) not only provides mechanical stability but also manipulates vascular cell behaviors, which are crucial for vascular function and homeostasis. ECM remodeling, which alters vascular wall mechanical properties and exposes vascular cells to bioactive molecules, is involved in the development and progression of hypertension. Recent Advances: This brief review summarized the dynamic changes in ECM components and their modification and degradation during hypertension and after antihypertensive treatment. We also discussed how alterations in the ECM amount, assembly, mechanical properties, and degradation fragment generation provide input into the pathological process of hypertension. Critical Issues: Although the relevance between ECM remodeling and hypertension has been recognized, the underlying mechanism by which ECM remodeling initiates the development of hypertension remains unclear. Therefore, the modulation of ECM remodeling on arterial stiffness and hypertension in genetically modified rodent models is summarized in this review. The circulating biomarkers based on ECM metabolism and therapeutic strategies targeting ECM disorders in hypertension are also introduced. Future Directions: Further research will provide more comprehensive understanding of ECM remodeling in hypertension by the application of matridomic and degradomic approaches. The better understanding of mechanisms underlying vascular ECM remodeling may provide novel potential therapeutic strategies for preventing and treating hypertension. Antioxid. Redox Signal. 34, 765-783.
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Affiliation(s)
- Zeyu Cai
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Beijing, China.,Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, China
| | - Ze Gong
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Beijing, China.,Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, China
| | - Zhiqing Li
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Beijing, China.,Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, China
| | - Li Li
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Beijing, China.,Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, China
| | - Wei Kong
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Beijing, China.,Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, China
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9
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Quantitative profiling of protease specificity. PLoS Comput Biol 2021; 17:e1008101. [PMID: 33617527 PMCID: PMC7932537 DOI: 10.1371/journal.pcbi.1008101] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 03/04/2021] [Accepted: 01/28/2021] [Indexed: 12/30/2022] Open
Abstract
Proteases are an important class of enzymes, whose activity is central to many physiologic and pathologic processes. Detailed knowledge of protease specificity is key to understanding their function. Although many methods have been developed to profile specificities of proteases, few have the diversity and quantitative grasp necessary to fully define specificity of a protease, both in terms of substrate numbers and their catalytic efficiencies. We have developed a concept of “selectome”; the set of substrate amino acid sequences that uniquely represent the specificity of a protease. We applied it to two closely related members of the Matrixin family–MMP-2 and MMP-9 by using substrate phage display coupled with Next Generation Sequencing and information theory-based data analysis. We have also derived a quantitative measure of substrate specificity, which accounts for both the number of substrates and their relative catalytic efficiencies. Using these advances greatly facilitates elucidation of substrate selectivity between closely related members of a protease family. The study also provides insight into the degree to which the catalytic cleft defines substrate recognition, thus providing basis for overcoming two of the major challenges in the field of proteolysis: 1) development of highly selective activity probes for studying proteases with overlapping specificities, and 2) distinguishing targeted proteolysis from bystander proteolytic events. Proteases and proteolysis are intimately involved in virtually all biological processes from embryonic development to programmed cell death and cellular protein recycling. As the only irreversible posttranslational modification, proteolysis represents a committed step in regulation of biological networks and pathways. Imbalance of proteolytic activity has catastrophic implications and is the basis of many genetic disorders as well as a multitude of pathological states of varying etiologies. To understand protease function, one must gain insight into the repertoires of substrates targeted by these enzymes. As many proteases recognize a wide variety of sequences in proteins, it is a challenge to establish if a particular cleavage represents a targeted or a bystander proteolytic event. In addition, since many proteases have overlapping specificities, especially among closely related members of the same gene families, it is a challenge to develop highly selective tools for studying or inhibition of these enzymes. In this work, we used two closely related proteases (MMP-2 and 9) as a model system for development of an information theory-based approach to quantification of substrate specificity and demonstrated its potential for distinguishing between the target and bystander proteolytic events as well as for uncovering selectivity between closely related proteases.
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10
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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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11
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Neves LX, Granato DC, Busso-Lopes AF, Carnielli CM, Patroni FMDS, De Rossi T, Oliveira AK, Ribeiro ACP, Brandão TB, Rodrigues AN, Lacerda PA, Uno M, Cervigne NK, Santos-Silva AR, Kowalski LP, Lopes MA, Paes Leme AF. Peptidomics-Driven Strategy Reveals Peptides and Predicted Proteases Associated With Oral Cancer Prognosis. Mol Cell Proteomics 2020; 20:100004. [PMID: 33578082 PMCID: PMC7950089 DOI: 10.1074/mcp.ra120.002227] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 10/26/2020] [Accepted: 11/11/2020] [Indexed: 12/11/2022] Open
Abstract
Protease activity has been associated with pathological processes that can lead to cancer development and progression. However, understanding the pathological unbalance in proteolysis is challenging because changes can occur simultaneously at protease, their inhibitor, and substrate levels. Here, we present a pipeline that combines peptidomics, proteomics, and peptidase predictions for studying proteolytic events in the saliva of 79 patients and their association with oral squamous cell carcinoma (OSCC) prognosis. Our findings revealed differences in the saliva peptidome of patients with (pN+) or without (pN0) lymph-node metastasis and delivered a panel of ten endogenous peptides correlated with poor prognostic factors plus five molecules able to classify pN0 and pN+ patients (area under the receiver operating characteristic curve > 0.85). In addition, endopeptidases and exopeptidases putatively implicated in the processing of differential peptides were investigated using cancer tissue gene expression data from public repositories, reinforcing their association with poorer survival rates and prognosis in oral cancer. The dynamics of the OSCC-related proteolysis were further explored via the proteomic profiling of saliva. This revealed that peptidase/endopeptidase inhibitors exhibited reduced levels in the saliva of pN+ patients, as confirmed by selected reaction monitoring-mass spectrometry, while minor changes were detected in the level of saliva proteases. Taken together, our results indicated that proteolytic activity is accentuated in the saliva of patients with OSCC and lymph-node metastasis and, at least in part, is modulated by reduced levels of salivary peptidase inhibitors. Therefore, this integrated pipeline provided better comprehension and discovery of molecular features with implications in the oral cancer metastasis prognosis.
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Affiliation(s)
- Leandro Xavier Neves
- Brazilian Biosciences National Laboratory, National Center for Research in Energy and Materials, Campinas, Brazil
| | - Daniela C Granato
- Brazilian Biosciences National Laboratory, National Center for Research in Energy and Materials, Campinas, Brazil
| | - Ariane Fidelis Busso-Lopes
- Brazilian Biosciences National Laboratory, National Center for Research in Energy and Materials, Campinas, Brazil
| | - Carolina M Carnielli
- Brazilian Biosciences National Laboratory, National Center for Research in Energy and Materials, Campinas, Brazil
| | - Fábio M de Sá Patroni
- Molecular Biology and Genetic Engineering Center, University of Campinas, Campinas, Brazil
| | - Tatiane De Rossi
- Brazilian Biosciences National Laboratory, National Center for Research in Energy and Materials, Campinas, Brazil
| | - Ana Karina Oliveira
- Brazilian Biosciences National Laboratory, National Center for Research in Energy and Materials, Campinas, Brazil
| | | | | | - André Nimtz Rodrigues
- Department of Head and Neck Surgery, Faculty of Medicine of Jundiaí, Jundiaí, Brazil
| | - Pammela Araujo Lacerda
- Department of Internal Medicine, Molecular Biology and Cell Culture Laboratory, Faculty of Medicine of Jundiaí, Jundiaí, Brazil
| | - Miyuki Uno
- Center for Translational Research in Oncology, São Paulo Cancer Institute, São Paulo, Brazil
| | - Nilva K Cervigne
- Department of Internal Medicine, Molecular Biology and Cell Culture Laboratory, Faculty of Medicine of Jundiaí, Jundiaí, Brazil
| | - Alan Roger Santos-Silva
- Oral Diagnosis Department, Piracicaba Dental School, University of Campinas, Piracicaba, São Paulo, Brazil
| | - Luiz Paulo Kowalski
- Head and Neck Surgery, Faculty of Medicine, University of São Paulo, São Paulo, Brazil
| | - Marcio Ajudarte Lopes
- Oral Diagnosis Department, Piracicaba Dental School, University of Campinas, Piracicaba, São Paulo, Brazil
| | - Adriana F Paes Leme
- Brazilian Biosciences National Laboratory, National Center for Research in Energy and Materials, Campinas, Brazil.
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12
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Abstract
INTRODUCTION The N-terminus of a protein can encode several protein features, including its half-live and its localization. As the proteomics field remains dominated by bottom-up approaches and as N-terminal peptides only account for a fraction of all analyzable peptides, there is a need for their enrichment prior to analysis. COFRADIC, TAILS, and the subtiligase method were among the first N-terminomics methods developed, and several variants and novel methods were introduced that often reduce processing time and/or the amount of material required. AREAS COVERED We present an overview of how the field of N-terminomics developed, including a discussion of the founding methods, several updates made to these and introduce newer methods such as TMPP-labeling, biotin-based methods besides some necessary improvements in data analysis. EXPERT OPINION N-terminomic methods remain being used and improved methods are published however, more efficient use of contemporary mass spectrometers, promising data-independent approaches, and mass spectrometry-free single peptide or protein sequences may threat the N-terminomics field.
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Affiliation(s)
- Annelies Bogaert
- VIB Center for Medical Biotechnology , Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University , Ghent, Belgium
| | - Kris Gevaert
- VIB Center for Medical Biotechnology , Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University , Ghent, Belgium
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13
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Limited Proteolysis of Cyclooxygenase-2 Enhances Cell Proliferation. Int J Mol Sci 2020; 21:ijms21093195. [PMID: 32366045 PMCID: PMC7246915 DOI: 10.3390/ijms21093195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 04/22/2020] [Accepted: 04/28/2020] [Indexed: 01/28/2023] Open
Abstract
Accumulating evidence suggests that the cyclooxygenase-2 (COX-2) enzyme has additional catalytic-independent functions. Here we show that COX-2 appears to be cleaved in mouse and human tumors, which led us to hypothesize that COX-2 proteolysis may play a role in cell proliferation. The data presented herein show that a K598R point mutation at the carboxyl-terminus of COX-2 causes the appearance of several COX-2 immunoreactive fragments in nuclear compartments, and significantly enhances cell proliferation. In contrast, insertion of additional mutations at the border of the membrane-binding and catalytic domains of K598R COX-2 blocks fragment formation and prevents the increase in proliferation. Transcriptomic analyses show that K598R COX-2 significantly affects the expression of genes involved in RNA metabolism, and subsequent proteomics suggest that it is associated with proteins that regulate mRNA processing. We observe a similar increase in proliferation by expressing just that catalytic domain of COX-2 (ΔNT- COX-2), which is completely devoid of catalytic activity in the absence of its other domains. Moreover, we show that the ΔNT- COX-2 protein also interacts in the nucleus with β-catenin, a central regulator of gene transcription. Together these data suggest that the cleavage products of COX-2 can affect cell proliferation by mechanisms that are independent of prostaglandin synthesis.
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Li L, Yan G, Zhang X. A rapid and efficient method for N-termini analysis in short-lived proteins. Talanta 2019; 204:367-371. [DOI: 10.1016/j.talanta.2019.06.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 06/02/2019] [Accepted: 06/08/2019] [Indexed: 02/05/2023]
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15
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Kirchhain A, Poma N, Salvo P, Tedeschi L, Melai B, Vivaldi F, Bonini A, Franzini M, Caponi L, Tavanti A, Di Francesco F. Biosensors for measuring matrix metalloproteinases: An emerging research field. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2018.10.027] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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16
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Magalhães B, Trindade F, Barros AS, Klein J, Amado F, Ferreira R, Vitorino R. Reviewing Mechanistic Peptidomics in Body Fluids Focusing on Proteases. Proteomics 2018; 18:e1800187. [DOI: 10.1002/pmic.201800187] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 06/13/2018] [Indexed: 01/07/2023]
Affiliation(s)
- Beatriz Magalhães
- Unidade de Investigação Cardiovascular; Departamento de Cirurgia e Fisiologia; Faculdade de Medicina da Universidade do Porto; 4200-319 Porto Portugal
| | - Fábio Trindade
- Unidade de Investigação Cardiovascular; Departamento de Cirurgia e Fisiologia; Faculdade de Medicina da Universidade do Porto; 4200-319 Porto Portugal
- Instituto de Biomedicina; Department of Medical Sciences; University of Aveiro; 3810-193 Aveiro Portugal
| | - António S. Barros
- Unidade de Investigação Cardiovascular; Departamento de Cirurgia e Fisiologia; Faculdade de Medicina da Universidade do Porto; 4200-319 Porto Portugal
| | - Julie Klein
- Institut National de la Santé et de la Recherche Médicale; Institute of Cardiovascular and Metabolic Disease; Toulouse France
- Université Toulouse III Paul-Sabatier; 31330 Toulouse France
| | - Francisco Amado
- Química Orgânica, Produtos Naturais e Agroalimentares; Department of Chemistry; University of Aveiro; 3810-193 Aveiro Portugal
| | - Rita Ferreira
- Química Orgânica, Produtos Naturais e Agroalimentares; Department of Chemistry; University of Aveiro; 3810-193 Aveiro Portugal
| | - Rui Vitorino
- Unidade de Investigação Cardiovascular; Departamento de Cirurgia e Fisiologia; Faculdade de Medicina da Universidade do Porto; 4200-319 Porto Portugal
- Instituto de Biomedicina; Department of Medical Sciences; University of Aveiro; 3810-193 Aveiro Portugal
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Vizovišek M, Vidmar R, Drag M, Fonović M, Salvesen GS, Turk B. Protease Specificity: Towards In Vivo Imaging Applications and Biomarker Discovery. Trends Biochem Sci 2018; 43:829-844. [PMID: 30097385 DOI: 10.1016/j.tibs.2018.07.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 06/05/2018] [Accepted: 07/12/2018] [Indexed: 02/06/2023]
Abstract
Proteases are considered of major importance in biomedical research because of their crucial roles in health and disease. Their ability to hydrolyze their protein and peptide substrates at single or multiple sites, depending on their specificity, makes them unique among the enzymes. Understanding protease specificity is therefore crucial to understand their biology as well as to develop tools and drugs. Recent advancements in the fields of proteomics and chemical biology have improved our understanding of protease biology through extensive specificity profiling and identification of physiological protease substrates. There are growing efforts to transfer this knowledge into clinical modalities, but their success is often limited because of overlapping protease features, protease redundancy, and chemical tools lacking specificity. Herein, we discuss the current trends and challenges in protease research and how to exploit the growing information on protease specificities for understanding protease biology, as well as for development of selective substrates, cleavable linkers, and activity-based probes and for biomarker discovery.
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Affiliation(s)
- Matej Vizovišek
- Jozef Stefan Institute, Department of Biochemistry and Molecular and Structural Biology, Jamova 39, SI-1000 Ljubljana, Slovenia; These authors contributed equally to this work
| | - Robert Vidmar
- Jozef Stefan Institute, Department of Biochemistry and Molecular and Structural Biology, Jamova 39, SI-1000 Ljubljana, Slovenia; These authors contributed equally to this work
| | - Marcin Drag
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Marko Fonović
- Jozef Stefan Institute, Department of Biochemistry and Molecular and Structural Biology, Jamova 39, SI-1000 Ljubljana, Slovenia
| | - Guy S Salvesen
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA.
| | - Boris Turk
- Jozef Stefan Institute, Department of Biochemistry and Molecular and Structural Biology, Jamova 39, SI-1000 Ljubljana, Slovenia; Faculty of Chemistry and Chemical Technology, University of Ljubljana, Vecna pot 113, SI-1000 Ljubljana, Slovenia.
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18
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Kalubowilage M, Covarrubias-Zambrano O, Malalasekera AP, Wendel SO, Wang H, Yapa AS, Chlebanowski L, Toledo Y, Ortega R, Janik KE, Shrestha TB, Culbertson CT, Kasi A, Williamson S, Troyer DL, Bossmann SH. Early detection of pancreatic cancers in liquid biopsies by ultrasensitive fluorescence nanobiosensors. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2018; 14:1823-1832. [PMID: 29782949 DOI: 10.1016/j.nano.2018.04.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 04/19/2018] [Accepted: 04/24/2018] [Indexed: 01/15/2023]
Abstract
Numerous proteases, such as matrix metalloproteinases (MMPs), cathepsins (CTS), and urokinase plasminogen activator (UpA), are dysfunctional (that is, over- or under-expressed) in solid tumors, when compared to healthy human subjects. This offers the opportunity to detect early tumors by liquid biopsies. This approach is of particular advantage for the early detection of pancreatic cancer, which is a "silent killer". We have developed fluorescence nanobiosensors for ultrasensitive (sub-femtomolar) arginase and protease detection, consisting of water-dispersible Fe/Fe3O4 core/shell nanoparticles and two tethered fluorescent dyes: TCPP (Tetrakis(4-carboxyphenyl)porphyrin) and cyanine 5.5. Upon posttranslational modification or enzymatic cleavage, the fluorescence of TCPP increases, which enables the detection of proteases at sub-femtomolar activities utilizing conventional plate readers. We have identified an enzymatic signature for the detection of pancreatic adenocarcinomas in serum, consisting of arginase, matrix metalloproteinase-1, -3, and - 9, cathepsin-B and -E, urokinase plasminogen activator, and neutrophil elastase, which is a potential game-changer.
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Affiliation(s)
| | | | | | - Sebastian O Wendel
- Department of Chemistry, Kansas State University, Manhattan, KS, USA; Department of Anatomy & Physiology, Kansas State University, Manhattan, KS, USA
| | - Hongwang Wang
- Department of Chemistry, Kansas State University, Manhattan, KS, USA
| | - Asanka S Yapa
- Department of Chemistry, Kansas State University, Manhattan, KS, USA
| | | | - Yubisela Toledo
- Department of Chemistry, Kansas State University, Manhattan, KS, USA
| | - Raquel Ortega
- Department of Chemistry, Kansas State University, Manhattan, KS, USA
| | - Katharine E Janik
- Department of Chemistry, Kansas State University, Manhattan, KS, USA
| | - Tej B Shrestha
- Department of Anatomy & Physiology, Kansas State University, Manhattan, KS, USA
| | | | - Anup Kasi
- University of Kansas Medical School, Kansas City, KS, USA
| | | | - Deryl L Troyer
- Department of Anatomy & Physiology, Kansas State University, Manhattan, KS, USA
| | - Stefan H Bossmann
- Department of Chemistry, Kansas State University, Manhattan, KS, USA.
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19
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Bridges RJ, Bradbury NA. Cystic Fibrosis, Cystic Fibrosis Transmembrane Conductance Regulator and Drugs: Insights from Cellular Trafficking. Handb Exp Pharmacol 2018; 245:385-425. [PMID: 29460152 DOI: 10.1007/164_2018_103] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The eukaryotic cell is organized into membrane-delineated compartments that are characterized by specific cadres of proteins sustaining biochemically distinct cellular processes. The appropriate subcellular localization of proteins is key to proper organelle function and provides a physiological context for cellular processes. Disruption of normal trafficking pathways for proteins is seen in several genetic diseases, where a protein's absence for a specific subcellular compartment leads to organelle disruption, and in the context of an individual, a disruption of normal physiology. Importantly, several drug therapies can also alter protein trafficking, causing unwanted side effects. Thus, a deeper understanding of trafficking pathways needs to be appreciated as novel therapeutic modalities are proposed. Despite the promising efficacy of novel therapeutic agents, the intracellular bioavailability of these compounds has proved to be a potential barrier, leading to failures in treatments for various diseases and disorders. While endocytosis of drug moieties provides an efficient means of getting material into cells, the subsequent release and endosomal escape of materials into the cytosol where they need to act has been a barrier. An understanding of cellular protein/lipid trafficking pathways has opened up strategies for increasing drug bioavailability. Approaches to enhance endosomal exit have greatly increased the cytosolic bioavailability of drugs and will provide a means of investigating previous drugs that may have been shelved due to their low cytosolic concentration.
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Affiliation(s)
- Robert J Bridges
- Department of Physiology and Biophysics, Chicago Medical School, North Chicago, IL, USA
| | - Neil A Bradbury
- Department of Physiology and Biophysics, Chicago Medical School, North Chicago, IL, USA.
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20
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Marciel MP, Rose AH, Martinez V, Horio DT, Hashimoto AS, Hoffmann FW, Bertino P, Hoffmann PR. Calpain-2 inhibitor treatment preferentially reduces tumor progression for human colon cancer cells expressing highest levels of this enzyme. Cancer Med 2017; 7:175-183. [PMID: 29210197 PMCID: PMC5773958 DOI: 10.1002/cam4.1260] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 10/05/2017] [Accepted: 10/15/2017] [Indexed: 12/18/2022] Open
Abstract
Calpain-2 levels are higher in colorectal tumors resistant to chemotherapy and previous work showed calpain-2 inhibitor therapy reduced inflammation-driven colorectal cancer, but direct effects of the inhibitor on colon cancer cells themselves were not demonstrated. In the present study, five human colon cancer cell lines were directly treated with a calpain-2 inhibitor and results showed increased cell death in 4 of 5 cell lines and decreased anchorage-independent growth for all cell five lines. When tested for levels of calpain-2, three cell lines exhibited increasing levels of this enzyme: HCT15 (low), HCC2998 (medium), and HCT116 (significantly higher). This was consistent with gel shift assays showing that calpain-2 inhibitor reduced of NF-κB nuclear translocation most effectively in HCT116 cells. Ability of calpain-2 inhibitor to impede tumor progression in vivo was evaluated using intrarectal transplant of luciferase-expressing cells for these three cell lines. Results showed that calpain-2 inhibitor therapy reduced tumor growth and increased survival only in mice injected with HCT116 cells. These data suggest calpain-2 inhibitor treatment may be most effective on colorectal tumors expressing highest levels of calpain-2.
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Affiliation(s)
- Michael P Marciel
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii
| | - Aaron H Rose
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii
| | - Verena Martinez
- Biotechnology Department, University of Applied Sciences Mannheim, Mannheim, Germany
| | - David T Horio
- Department of Pathology, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii
| | - Ann S Hashimoto
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii
| | - FuKun W Hoffmann
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii
| | - Pietro Bertino
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii
| | - Peter R Hoffmann
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii
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21
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Li J, Qin Y, Zhang H. Identification of key miRNA-gene pairs in chronic lymphocytic leukemia through integrated analysis of mRNA and miRNA microarray. Oncol Lett 2017; 15:361-367. [PMID: 29285196 PMCID: PMC5738675 DOI: 10.3892/ol.2017.7287] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 10/17/2017] [Indexed: 12/17/2022] Open
Abstract
The aim of the present study was to explore the miRNA-Gene regulatory mechanism in chronic lymphocytic leukemia (CLL), and identify new targets for the therapy of CLL. The miRNA expression dataset GSE62137 and mRNA expression dataset GSE22529 were downloaded from National Center of Biotechnology Information Gene Expression Omnibus database. In CLL samples compared with normal B cell samples, differentially expressed miRNAs (DEMs) were identified via the GEO2R instrument of GEO and differentially expressed genes (DEGs) were obtained via the limma package of R. Functional enrichment analysis of the DEGs was performed via the Database for Annotation, Visualization and Integrated Discovery. The targets of the DEMs were identified based on the miRNAWalk platform. The overlaps between the DEGs and the targets of the DEMs were selected, and the miRNA-Gene regulatory network was constructed based on the overlaps and the corresponding DEMs. A total of 63 DEMs and 504 DEGs were identified in CLL samples compared with normal B cell samples. Eleven enriched functional clusters of the DEGs were obtained. 405 miRNA-Gene regulatory pairs were identified. The miRNA-Gene regulatory pairs contained 351 target genes of the DEMs, including 9 overlaps with the DEGs. A miRNA-Gene regulatory network was constructed. Bioinformatics methods could help us develop a better understanding of the molecular mechanism of CLL. MiRNAs may play a critical role in regulating the process of CLL. They may affect CLL by regulating the processes of immunoreactivity and protein degradation. Genes such as Neurogenic Locus Notch Homolog Protein 2, PR/SET domain 4 and A-kinase anchoring protein 12 may be their regulating targets in CLL.
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Affiliation(s)
- Jie Li
- Department of Transfusion Medicine, The Fifth Central Hospital of Tianjin, Tianjin 300450, P.R. China
| | - Yi Qin
- Institute of Medical Laboratory, Tianjin Medical University, Tianjin 300072, P.R. China
| | - Haiyan Zhang
- Department of Medical Record Management, The Fifth Central Hospital of Tianjin, Tianjin 300450, P.R. China
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22
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Abou-El-Hassan H, Sukhon F, Assaf EJ, Bahmad H, Abou-Abbass H, Jourdi H, Kobeissy FH. Degradomics in Neurotrauma: Profiling Traumatic Brain Injury. Methods Mol Biol 2017; 1598:65-99. [PMID: 28508358 DOI: 10.1007/978-1-4939-6952-4_4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Degradomics has recently emerged as a subdiscipline in the omics era with a focus on characterizing signature breakdown products implicated in various disease processes. Driven by promising experimental findings in cancer, neuroscience, and metabolomic disorders, degradomics has significantly promoted the notion of disease-specific "degradome." A degradome arises from the activation of several proteases that target specific substrates and generate signature protein fragments. Several proteases such as calpains, caspases, cathepsins, and matrix metalloproteinases (MMPs) are involved in the pathogenesis of numerous diseases that disturb the physiologic balance between protein synthesis and protein degradation. While regulated proteolytic activities are needed for development, growth, and regeneration, uncontrolled proteolysis initiated under pathological conditions ultimately culminates into apoptotic and necrotic processes. In this chapter, we aim to review the protease-substrate repertoires in neural injury concentrating on traumatic brain injury. A striking diversity of protease substrates, essential for neuronal and brain structural and functional integrity, namely, encryptic biomarker neoproteins, have been characterized in brain injury. These include cytoskeletal proteins, transcription factors, cell cycle regulatory proteins, synaptic proteins, and cell junction proteins. As these substrates are subject to proteolytic fragmentation, they are ceaselessly exposed to activated proteases. Characterization of these molecules allows for a surge of "possible" therapeutic approaches of intervention at various levels of the proteolytic cascade.
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Affiliation(s)
- Hadi Abou-El-Hassan
- Faculty of Medicine, American University of Beirut Medical Center, Beirut, Lebanon.
| | - Fares Sukhon
- Faculty of Medicine, Department of Internal Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Edwyn Jeremy Assaf
- Faculty of Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Hisham Bahmad
- Faculty of Medical, Neuroscience Research Center, Beirut Arab University, Beirut, Lebanon
- Faculty of Medicine, Department of Anatomy, Cell Biology and Physiological Sciences, American University of Beirut, Beirut, Lebanon
| | - Hussein Abou-Abbass
- Faculty of Medical Sciences, Neuroscience Research Center, Lebanese University, Beirut, Lebanon
- Faculty of Medicine, Department of Biochemistry and Molecular Genetics, American University of Beirut, Beirut, Lebanon
| | - Hussam Jourdi
- Faculty of Science¸ Department of Biology, University of Balamand, Souk-el-Gharb Campus, Aley, Lebanon
| | - Firas H Kobeissy
- Faculty of Medicine, Department of Biochemistry and Molecular Genetics, American University of Beirut, Beirut, Lebanon.
- Department of Psychiatry, Center for Neuroproteomics and Biomarkers Research, University of Florida, Gainesville, FL, USA.
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23
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Bingeman TS, Perlman DH, Storey DG, Lewis IA. Digestomics: an emerging strategy for comprehensive analysis of protein catabolism. Curr Opin Biotechnol 2016; 43:134-140. [PMID: 28025112 DOI: 10.1016/j.copbio.2016.11.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Revised: 11/01/2016] [Accepted: 11/04/2016] [Indexed: 11/29/2022]
Abstract
When cells mobilize nutrients from protein, they generate a fingerprint of peptide fragments that reflects the net action of proteases and the identities of the affected proteins. Analyzing these mixtures falls into a grey area between proteomics and metabolomics that is poorly served by existing technology. Herein, we describe an emerging digestomics strategy that bridges this gap and allows mixtures of proteolytic fragments to be quantitatively mapped with an amino acid level of resolution. We describe recent successes using this technique, including a case where digestomics provided the link between hemoglobin digestion by the malaria parasite and the world-wide distribution of chloroquine resistance. We highlight other areas of microbiology and cancer research that are well-suited to this emerging technology.
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Affiliation(s)
- Travis S Bingeman
- Department of Biological Science, University of Calgary, 2500 University Dr NW, Calgary, AB, Canada T2N 1N4
| | - David H Perlman
- Department of Biological Science, University of Calgary, 2500 University Dr NW, Calgary, AB, Canada T2N 1N4
| | - Douglas G Storey
- Department of Biological Science, University of Calgary, 2500 University Dr NW, Calgary, AB, Canada T2N 1N4
| | - Ian A Lewis
- Department of Biological Science, University of Calgary, 2500 University Dr NW, Calgary, AB, Canada T2N 1N4.
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24
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Butler GS, Connor AR, Sounni NE, Eckhard U, Morrison CJ, Noël A, Overall CM. Degradomic and yeast 2-hybrid inactive catalytic domain substrate trapping identifies new membrane-type 1 matrix metalloproteinase (MMP14) substrates: CCN3 (Nov) and CCN5 (WISP2). Matrix Biol 2016; 59:23-38. [PMID: 27471094 DOI: 10.1016/j.matbio.2016.07.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 07/19/2016] [Accepted: 07/19/2016] [Indexed: 12/20/2022]
Abstract
Members of the CCN family of matricellular proteins are cytokines linking cells to the extracellular matrix. We report that CCN3 (Nov) and CCN5 (WISP2) are novel substrates of MMP14 (membrane-type 1-matrix metalloproteinase, MT1-MMP) that we identified using MMP14 "inactive catalytic domain capture" (ICDC) as a yeast two-hybrid protease substrate trapping platform in parallel with degradomics mass spectrometry screens for MMP14 substrates. CCN3 and CCN5, previously unknown substrates of MMPs, were biochemically validated as substrates of MMP14 and other MMPs in vitro-CCN5 was processed in the variable region by MMP14 and MMP2, as well as by MMP1, 3, 7, 8, 9 and 15. CCN1, 2 and 3 are proangiogenic factors yet we found novel opposing activity of CCN5 that was potently antiangiogenic in an aortic ring vessel outgrowth model. MMP14, a known regulator of angiogenesis, cleaved CCN5 and abrogated the angiostatic activity. CCN3 was also processed in the variable region by MMP14 and MMP2, and by MMP1, 8 and 9. In addition to the previously reported cleavages of CCN1 and CCN2 by several MMPs we found that MMPs 8, 9, and 1 process CCN1, and MMP8 and MMP9 also process CCN2. Thus, our study reveals additional and pervasive family-wide processing of CCN matricellular proteins/cytokines by MMPs. Furthermore, CCN5 cleavage by proangiogenic MMPs results in removal of an angiogenic brake held by CCN5. This highlights the importance of thorough dissection of MMP substrates that is needed to reveal higher-level control mechanisms beyond type IV collagen and other extracellular matrix protein remodelling in angiogenesis. SUMMARY We find CCN family member cleavage by MMPs is more pervasive than previously reported and includes CCN3 (Nov) and CCN5 (WISP2). CCN5 is a novel antiangiogenic factor, whose function is abrogated by proangiogenic MMP cleavage. By processing CCN proteins, MMPs regulate cell responses angiogenesis in connective tissues.
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Affiliation(s)
- Georgina S Butler
- Centre for Blood Research, Departments of Oral Biological & Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, Canada
| | - Andrea R Connor
- Centre for Blood Research, Departments of Oral Biological & Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, Canada
| | - Nor Eddine Sounni
- Centre for Blood Research, Departments of Oral Biological & Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, Canada
| | - Ulrich Eckhard
- Centre for Blood Research, Departments of Oral Biological & Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, Canada
| | - Charlotte J Morrison
- Centre for Blood Research, Departments of Oral Biological & Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, Canada
| | - Agnès Noël
- Centre for Blood Research, Departments of Oral Biological & Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, Canada
| | - Christopher M Overall
- Centre for Blood Research, Departments of Oral Biological & Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, Canada.
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25
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A bead-based cleavage method for large-scale identification of protease substrates. Sci Rep 2016; 6:22645. [PMID: 26935269 PMCID: PMC4776233 DOI: 10.1038/srep22645] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 02/16/2016] [Indexed: 01/25/2023] Open
Abstract
Proteolysis is a major form of post translational modification which occurs when a protease cleaves peptide bonds in a target protein to modify its activity. Tracking protease substrates is indispensable for understanding its cellular functions. However, it is difficult to directly identify protease substrates because the end products of proteolysis, the cleaved protein fragments, must be identified among the pool of cellular proteins. Here we present a bead-based cleavage approach using immobilized proteome as the screening library to identify protease substrates. This method enables efficient separation of proteolyzed proteins from background protein mixture. Using caspase-3 as the model protease, we have identified 1159 high confident substrates, among which, strikingly, 43.9% of substrates undergo degradation during apoptosis. The huge number of substrates and positive support of in vivo evidence indicate that the BBC method is a powerful tool for protease substrates identification.
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26
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Vizovišek M, Vidmar R, Fonović M, Turk B. Current trends and challenges in proteomic identification of protease substrates. Biochimie 2016; 122:77-87. [DOI: 10.1016/j.biochi.2015.10.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 10/23/2015] [Indexed: 10/22/2022]
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27
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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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Rut W, Kasperkiewicz P, Byzia A, Poreba M, Groborz K, Drag M. Recent advances and concepts in substrate specificity determination of proteases using tailored libraries of fluorogenic substrates with unnatural amino acids. Biol Chem 2015; 396:329-37. [PMID: 25719315 DOI: 10.1515/hsz-2014-0315] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 01/27/2015] [Indexed: 11/15/2022]
Abstract
Substrate specificity of proteases can be determined using several methods among which the most frequently used are positional scanning library, proteomics and phage display. Classic approaches can deliver information about preferences for natural amino acids in binding pockets of virtually all proteases. However, recent studies demonstrate the ability to obtain much more information by application of unnatural amino acids to positional scanning library approaches. This knowledge can be used for the design of more active and specific substrates, inhibitors and activity based probes. In this minireview we describe recent strategies and concepts for the design and application of fluorogenic substrates library tailored for exopeptidases and endopeptidases.
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Verbovšek U, Van Noorden CJ, Lah TT. Complexity of cancer protease biology: Cathepsin K expression and function in cancer progression. Semin Cancer Biol 2015; 35:71-84. [DOI: 10.1016/j.semcancer.2015.08.010] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 08/19/2015] [Accepted: 08/21/2015] [Indexed: 12/18/2022]
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Berry IJ, Steele JR, Padula MP, Djordjevic SP. The application of terminomics for the identification of protein start sites and proteoforms in bacteria. Proteomics 2015; 16:257-72. [DOI: 10.1002/pmic.201500319] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 09/21/2015] [Accepted: 09/30/2015] [Indexed: 01/11/2023]
Affiliation(s)
- Iain J. Berry
- The ithree Institute; University of Technology Sydney; Broadway NSW Australia
- Proteomics Core Facility; University of Technology Sydney; Broadway NSW Australia
| | - Joel R. Steele
- Proteomics Core Facility; University of Technology Sydney; Broadway NSW Australia
| | - Matthew P. Padula
- The ithree Institute; University of Technology Sydney; Broadway NSW Australia
- Proteomics Core Facility; University of Technology Sydney; Broadway NSW Australia
| | - Steven P. Djordjevic
- The ithree Institute; University of Technology Sydney; Broadway NSW Australia
- Proteomics Core Facility; University of Technology Sydney; Broadway NSW Australia
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31
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Li L, Wu R, Yan G, Gao M, Deng C, Zhang X. A novel method to isolate protein N-terminal peptides from proteome samples using sulfydryl tagging and gold-nanoparticle-based depletion. Anal Bioanal Chem 2015; 408:441-8. [DOI: 10.1007/s00216-015-9136-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 10/15/2015] [Accepted: 10/20/2015] [Indexed: 12/18/2022]
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Kanost MR, Jiang H. Clip-domain serine proteases as immune factors in insect hemolymph. CURRENT OPINION IN INSECT SCIENCE 2015; 11:47-55. [PMID: 26688791 PMCID: PMC4680995 DOI: 10.1016/j.cois.2015.09.003] [Citation(s) in RCA: 161] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
CLIP proteases are non-digestive serine proteases present in hemolymph of insects and other arthropods. They are composed of one or more amino-terminal clip domains followed by a linker sequence and a carboxyl-terminal S1A family serine protease domain. The genes for CLIP proteases have evolved as four clades (CLIPA, CLIPB, CLIPC, CLIPD), each present as multigene families in insect genomes. CLIP proteases in hemolymph function in innate immune responses. These include proteolytic activation of the cytokine Spätzle, to form an active Toll ligand leading to synthesis of antimicrobial peptides, and specific activation of prophenoloxidase, required for the melanization response. CLIP proteases act in cascade pathways. In the immune pathways that have been characterized, microbial surface molecules stimulate activation of an initiating modular serine protease, which then activates a CLIPC, which in turn activates a CLIPB. The active CLIPB then cleaves and activates an effector molecule (proSpätzle or prophenoloxidase). CLIPA proteins are pseudoproteases, lacking proteolytic activity, but some can function as regulators of the activity of other CLIP proteases and form high molecular weight immune complexes. A few three dimensional structures for CLIP proteases are now available for structure-function analysis of these immune factors, revealing structural features that may act in specific activation or in formation of immune complexes. The functions of most CLIP proteases are unknown, even in well studied insect species. It is very likely that additional proteins activated by CLIP proteases and acting in immunity remain to be discovered.
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Affiliation(s)
- Michael R. Kanost
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506 USA
- Communicating author: Michael R. Kanost, Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506 USA, 785-532-6964,
| | - Haobo Jiang
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK, 74078 USA
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33
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Marino G, Eckhard U, Overall CM. Protein Termini and Their Modifications Revealed by Positional Proteomics. ACS Chem Biol 2015; 10:1754-64. [PMID: 26042555 DOI: 10.1021/acschembio.5b00189] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A myriad of co- and post-translational modifications occur at protein N- and C-termini, resulting in an extra layer of proteome complexity and an additional source of protein regulation. Here, we review N- and C-terminal modifications and the contemporary positional proteomics techniques used to isolate protein terminal peptides from complex protein mixtures and characterize their diversity and occurrence in biological systems. Furthermore, these degradomics strategies--often referred to as N- and C-terminomics--represent dedicated high-throughput techniques to study proteolysis in dynamic living systems. Over the past decade, terminomics studies have provided indispensable information on the functional states of individual proteins, cell types, tissues, and biological processes and delivered fundamental new data for the Human Proteome Project, including high confidence identifications of many so-called "missing proteins", which had not been identified by traditional proteomics analyses.
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Affiliation(s)
- Giada Marino
- Centre
for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Ulrich Eckhard
- Centre
for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Christopher M. Overall
- Centre
for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- Department
of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
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34
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Kukreja M, Shiryaev SA, Cieplak P, Muranaka N, Routenberg DA, Chernov AV, Kumar S, Remacle AG, Smith JW, Kozlov IA, Strongin AY. High-Throughput Multiplexed Peptide-Centric Profiling Illustrates Both Substrate Cleavage Redundancy and Specificity in the MMP Family. ACTA ACUST UNITED AC 2015; 22:1122-33. [PMID: 26256476 DOI: 10.1016/j.chembiol.2015.07.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 06/18/2015] [Accepted: 07/08/2015] [Indexed: 10/23/2022]
Abstract
Matrix metalloproteinases (MMPs) play incompletely understood roles in health and disease. Knowing the MMP cleavage preferences is essential for a better understanding of the MMP functions and design of selective inhibitors. To elucidate the cleavage preferences of MMPs, we employed a high-throughput multiplexed peptide-centric profiling technology involving the cleavage of 18,583 peptides by 18 proteinases from the main sub-groups of the MMP family. Our results enabled comparison of the MMP substrates on a global scale, leading to the most efficient and selective substrates. The data validated the accuracy of our cleavage prediction software. This software allows us and others to locate, with nearly 100% accuracy, the MMP cleavage sites in the peptide sequences. In addition to increasing our understanding of both the selectivity and the redundancy of the MMP family, our study generated a roadmap for the subsequent MMP structural-functional studies and efficient substrate and inhibitor design.
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Affiliation(s)
| | - Sergey A Shiryaev
- Infectious and Inflammatory Disease Center/Cancer Research Center, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Piotr Cieplak
- Infectious and Inflammatory Disease Center/Cancer Research Center, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | | | | | - Andrei V Chernov
- Infectious and Inflammatory Disease Center/Cancer Research Center, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Sonu Kumar
- Infectious and Inflammatory Disease Center/Cancer Research Center, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Albert G Remacle
- Infectious and Inflammatory Disease Center/Cancer Research Center, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Jeffrey W Smith
- Infectious and Inflammatory Disease Center/Cancer Research Center, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Igor A Kozlov
- Prognosys Biosciences Inc., San Diego, CA 92121, USA
| | - Alex Y Strongin
- Infectious and Inflammatory Disease Center/Cancer Research Center, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA.
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35
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Brix K, McInnes J, Al-Hashimi A, Rehders M, Tamhane T, Haugen MH. Proteolysis mediated by cysteine cathepsins and legumain-recent advances and cell biological challenges. PROTOPLASMA 2015; 252:755-774. [PMID: 25398648 DOI: 10.1007/s00709-014-0730-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 11/04/2014] [Indexed: 06/04/2023]
Abstract
Proteases play essential roles in protein degradation, protein processing, and extracellular matrix remodeling in all cell types and tissues. They are also involved in protein turnover for maintenance of homeostasis and protein activation or inactivation for cell signaling. Proteases range in function and specificity, with some performing distinct substrate cleavages, while others accomplish proteolysis of a wide range of substrates. As such, different cell types use specialized molecular mechanisms to regulate the localization of proteases and their function within the compartments to which they are destined. Here, we focus on the cysteine family of cathepsin proteases and legumain, which act predominately within the endo-lysosomal pathway. In particular, recent knowledge on cysteine cathepsins and their primary regulator legumain is scrutinized in terms of their trafficking to endo-lysosomal compartments and other less recognized cellular locations. We further explore the mechanisms that regulate these processes and point to pathological cases which arise from detours taken by these proteases. Moreover, the emerging biological roles of specific forms and variants of cysteine cathepsins and legumain are discussed. These may be decisive, pathogenic, or even deadly when localizing to unusual cellular compartments in their enzymatically active form, because they may exert unexpected effects by alternative substrate cleavage. Hence, we propose future perspectives for addressing the actions of cysteine cathepsins and legumain as well as their specific forms and variants. The increasing knowledge in non-canonical aspects of cysteine cathepsin- and legumain-mediated proteolysis may prove valuable for developing new strategies to utilize these versatile proteases in therapeutic approaches.
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Affiliation(s)
- Klaudia Brix
- Research Area HEALTH, Research Center MOLIFE-Molecular Life Sciences, Jacobs University Bremen, Campus Ring 1, 28759, Bremen, Germany,
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36
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Tsiatsiani L, Heck AJR. Proteomics beyond trypsin. FEBS J 2015; 282:2612-26. [PMID: 25823410 DOI: 10.1111/febs.13287] [Citation(s) in RCA: 221] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 03/19/2015] [Accepted: 03/26/2015] [Indexed: 12/13/2022]
Abstract
Peptide-centered shotgun analysis of proteins has been the core technology in mass spectrometry based proteomics and has enabled numerous biological discoveries, such as the large-scale charting of protein-protein interaction networks, the quantitative analysis of protein post-translational modifications and even the first drafts of the human proteome. The conversion of proteins into peptides in these so-called bottom-up approaches is nearly uniquely done by using trypsin as a proteolytic reagent. Here, we argue that our view of the proteome still remains incomplete and this is partially due to the nearly exclusive use of trypsin. Newly emerging alternative proteases and/or multi-protease protein digestion aim to increase proteome sequence coverage and improve the identification of post-translational modifications, through the analysis of complementary and often longer peptides, introducing an approach termed middle-down proteomics. Of pivotal importance for this purpose is the identification of proteases beneficial for use in proteomics. Here, we describe some of the shortcomings of the nearly exclusive use of trypsin in proteomics and review the properties of other proteomics-appropriate proteases. We describe favorable protease traits with an emphasis on middle-down proteomics and suggest potential sources for the discovery of new proteases. We also highlight a few examples wherein the use of other proteases than trypsin enabled the generation of more comprehensive data sets leading to previously unexplored knowledge of the proteome.
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Affiliation(s)
- Liana Tsiatsiani
- Biomolecular Mass Spectrometry and Proteomics Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Netherlands Proteomics Center, The Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Netherlands Proteomics Center, The Netherlands
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37
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TAILS N-terminomics of human platelets reveals pervasive metalloproteinase-dependent proteolytic processing in storage. Blood 2014; 124:e49-60. [PMID: 25331112 DOI: 10.1182/blood-2014-04-569640] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Proteases, and specifically metalloproteinases, have been linked to the loss of platelet function during storage before transfusion, but the underlying mechanisms remain unknown. We used a dedicated N-terminomics technique, iTRAQ terminal amine isotopic labeling of substrates (TAILS), to characterize the human platelet N-terminome, proteome, and posttranslational modifications throughout platelet storage over 9 days under blood-banking conditions. From the identified 2938 proteins and 7503 unique peptides, we characterized N-terminal methionine excision, co- and posttranslational Nα acetylation, protein maturation, and proteolytic processing of proteins in human platelets. We also identified for the first time 10 proteins previously classified by the Human Proteome Organization as "missing" in the human proteome. Most N termini (77%) were internal neo-N termini (105 were novel potential alternative translation start sites, and 2180 represented stable proteolytic products), thus highlighting a prominent yet previously uncharacterized role of proteolytic processing during platelet storage. Protease inhibitor studies revealed metalloproteinases as being primarily responsible for proteolytic processing (as opposed to degradation) during storage. System-wide identification of metalloproteinase and other proteinase substrates and their respective cleavage sites suggests novel mechanisms of the effect of proteases on protein activity and platelet function during storage. All data sets and metadata are available through ProteomeXchange with the data set identifier PXD000906.
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38
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Myocardial matrix metalloproteinase-2: inside out and upside down. J Mol Cell Cardiol 2014; 77:64-72. [PMID: 25261607 DOI: 10.1016/j.yjmcc.2014.09.016] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 08/19/2014] [Accepted: 09/10/2014] [Indexed: 12/31/2022]
Abstract
Since their inaugural discovery in the early 1960s, matrix metalloproteinases (MMPs) have been shown to mediate multiple physiological and pathological processes. In addition to their canonical function in extracellular matrix (ECM) remodeling, research in the last decade has highlighted new MMP functions, including proteolysis of novel substrates beyond ECM proteins, MMP localization to subcellular organelles, and proteolysis of susceptible intracellular proteins in those subcellular compartments. This review will provide a comparison of the extracellular and intracellular roles of MMPs, illustrating that MMPs are far more interesting than the one-dimensional view originally taken. We focus on the roles of MMP-2 in cardiac injury and repair, as this is one of the most studied MMPs in the cardiovascular field. We will highlight how understanding all dimensions, such as localization of activity and timing of interventions, will increase the translational potential of research findings. Building upon old ideas and turning them inside out and upside down will help us to better understand how to move the MMP field forward.
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Bauça JM, Martínez-Morillo E, Diamandis EP. Peptidomics of Urine and Other Biofluids for Cancer Diagnostics. Clin Chem 2014; 60:1052-61. [DOI: 10.1373/clinchem.2013.211714] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Abstract
BACKGROUND
Cancer is a leading cause of death worldwide. The low diagnostic sensitivity and specificity of most current cancer biomarkers make early cancer diagnosis a challenging task. The comprehensive study of peptides and small proteins in a living system, known as “peptidomics,” represents an alternative technological approach to the discovery of potential biomarkers for the assessment of a wide variety of pathologies. This review examines the current status of peptidomics for several body fluids, with a focus on urine, for cancer diagnostics applications.
CONTENT
Several studies have used high-throughput technologies to characterize the peptide content of different body fluids. Because of its noninvasive collection and high stability, urine is a valuable source of candidate cancer biomarkers. A wide variety of preanalytical issues concerning patient selection and sample handling need to be considered, because not doing so can affect the quality of the results by introducing bias and artifacts. Optimization of both the analytical strategies and the processing of bioinformatics data is also essential to minimize the false-discovery rate.
SUMMARY
Peptidomics-based studies of urine and other body fluids have yielded a number of biomolecules and peptide panels with potential for diagnosing different types of cancer, especially of the ovary, prostate, and bladder. Large-scale studies are needed to validate these molecules as cancer biomarkers.
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Affiliation(s)
- Josep Miquel Bauça
- Servei d'Anàlisis Clíniques, Hospital Universitari Son Espases, Palma de Mallorca, Spain
| | - Eduardo Martínez-Morillo
- Samuel Lunenfeld Research Institute, Joseph and Wolf Lebovic Health Centre, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Eleftherios P Diamandis
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Department of Clinical Biochemistry, Toronto General Hospital, University Health Network, Toronto, Ontario, Canada
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
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40
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Glibert P, Vossaert L, Van Steendam K, Lambrecht S, Van Nieuwerburgh F, Offner F, Kipps T, Dhaenens M, Deforce D. Quantitative proteomics to characterize specific histone H2A proteolysis in chronic lymphocytic leukemia and the myeloid THP-1 cell line. Int J Mol Sci 2014; 15:9407-21. [PMID: 24871368 PMCID: PMC4100102 DOI: 10.3390/ijms15069407] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Revised: 04/30/2014] [Accepted: 05/21/2014] [Indexed: 01/01/2023] Open
Abstract
Proteome studies on hematological malignancies contribute to the understanding of the disease mechanism and to the identification of new biomarker candidates. With the isobaric tag for relative and absolute quantitation (iTRAQ) method we analyzed the protein expression between B-cells of healthy people and chronic lymphocytic leukemia (CLL) B-cells. CLL is the most common lymphoid cancer of the blood and is characterized by a variable clinical course. By comparing samples of patients with an aggressive vs. indolent disease, we identified a limited list of differentially regulated proteins. The enhanced sensitivity attributed to the iTRAQ labels led to the discovery of a previously reported but still not clarified proteolytic product of histone H2A (cH2A) which we further investigated in light of the suggested functional properties of this modification. In the exploratory proteome study the Histone H2A peptide was up-regulated in CLL samples but a more specific and sensitive screening of a larger patient cohort indicated that cH2A is of myeloid origin. Our subsequent quantitative analysis led to a more profound characterization of the clipping in acute monocytic leukemia THP-1 cells subjected to induced differentiation.
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MESH Headings
- Amino Acid Sequence
- B-Lymphocytes/metabolism
- B-Lymphocytes/pathology
- Gene Expression Regulation, Leukemic
- Histones/analysis
- Histones/genetics
- Histones/metabolism
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/metabolism
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Middle Aged
- Molecular Sequence Data
- Proteolysis
- Proteomics/methods
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Affiliation(s)
- Pieter Glibert
- Laboratory of Pharmaceutical Biotechnology, Ghent University, 72 Harelbekestraat, B-9000 Ghent, Belgium.
| | - Liesbeth Vossaert
- Laboratory of Pharmaceutical Biotechnology, Ghent University, 72 Harelbekestraat, B-9000 Ghent, Belgium.
| | - Katleen Van Steendam
- Laboratory of Pharmaceutical Biotechnology, Ghent University, 72 Harelbekestraat, B-9000 Ghent, Belgium.
| | - Stijn Lambrecht
- Department of Rheumatology, Ghent University Hospital, 185 1P7 De Pintelaan, B-9000 Ghent, Belgium.
| | - Filip Van Nieuwerburgh
- Laboratory of Pharmaceutical Biotechnology, Ghent University, 72 Harelbekestraat, B-9000 Ghent, Belgium.
| | - Fritz Offner
- Department of Hematology, Ghent University Hospital, 185 1P7 De Pintelaan, B-9000 Ghent, Belgium.
| | - Thomas Kipps
- Department of Medicine, Moores Cancer Center, University of California at San Diego (UCSD), 3855 Health Sciences Drive, La Jolla, CA 92093, USA.
| | - Maarten Dhaenens
- Laboratory of Pharmaceutical Biotechnology, Ghent University, 72 Harelbekestraat, B-9000 Ghent, Belgium.
| | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Ghent University, 72 Harelbekestraat, B-9000 Ghent, Belgium.
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Network analyses reveal pervasive functional regulation between proteases in the human protease web. PLoS Biol 2014; 12:e1001869. [PMID: 24865846 PMCID: PMC4035269 DOI: 10.1371/journal.pbio.1001869] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 04/16/2014] [Indexed: 11/21/2022] Open
Abstract
Network modeling of interactions between proteases and their inhibitors reveals a network of new protein connections and cascades in the protease web. Proteolytic processing is an irreversible posttranslational modification affecting a large portion of the proteome. Protease-cleaved mediators frequently exhibit altered activity, and biological pathways are often regulated by proteolytic processing. Many of these mechanisms have not been appreciated as being protease-dependent, and the potential in unraveling a complex new dimension of biological control is increasingly recognized. Proteases are currently believed to act individually or in isolated cascades. However, conclusive but scattered biochemical evidence indicates broader regulation of proteases by protease and inhibitor interactions. Therefore, to systematically study such interactions, we assembled curated protease cleavage and inhibition data into a global, computational representation, termed the protease web. This revealed that proteases pervasively influence the activity of other proteases directly or by cleaving intermediate proteases or protease inhibitors. The protease web spans four classes of proteases and inhibitors and so links both recently and classically described protease groups and cascades, which can no longer be viewed as operating in isolation in vivo. We demonstrated that this observation, termed reachability, is robust to alterations in the data and will only increase in the future as additional data are added. We further show how subnetworks of the web are operational in 23 different tissues reflecting different phenotypes. We applied our network to develop novel insights into biologically relevant protease interactions using cell-specific proteases of the polymorphonuclear leukocyte as a system. Predictions from the protease web on the activity of matrix metalloproteinase 8 (MMP8) and neutrophil elastase being linked by an inactivating cleavage of serpinA1 by MMP8 were validated and explain perplexing Mmp8−/− versus wild-type polymorphonuclear chemokine cleavages in vivo. Our findings supply systematically derived and validated evidence for the existence of the protease web, a network that affects the activity of most proteases and thereby influences the functional state of the proteome and cell activity. Proteases modify the structure and activity of all proteins by peptide bond hydrolysis and are increasingly recognized as integral regulatory components of numerous biological mechanisms. Deregulated protease activity is a common characteristic of many diseases. However, protease drug development is complicated by an incomplete understanding of protease biology. One missing piece in this puzzle is the interplay between proteases: Some proteases activate other proteases, whereas some proteases inactivate inhibitors, leading to currently unpredictable cleavage of additional proteins. Using database annotations we mathematically modeled protease interactions. Our model includes 1,230 proteins and shows connections between 141,523 pairs of proteases, substrates, and inhibitors. Thus, proteases interact on a large scale to form the protease web, which links most studied groups of proteases and their inhibitors, indicating that the potential of regulation through this network is very large. We found that this interplay is robust to targeted or untargeted pruning of the protease web and that protease inhibitors are central to network connectivity. Our model was used to decipher proteolytic pathways that drive inflammatory processes in vivo. Consequently, protease regulatory interactions should be recognized and explored further to understand in vivo roles and to select better drug targets that avoid side effects arising from inhibition of unexpected activities.
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42
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Granato DC, Zanetti MR, Kawahara R, Yokoo S, Domingues RR, Aragão AZ, Agostini M, Carazzolle MF, Vidal RO, Flores IL, Korvala J, Cervigne NK, Silva ARS, Coletta RD, Graner E, Sherman NE, Leme AFP. Integrated proteomics identified up-regulated focal adhesion-mediated proteins in human squamous cell carcinoma in an orthotopic murine model. PLoS One 2014; 9:e98208. [PMID: 24858105 PMCID: PMC4032327 DOI: 10.1371/journal.pone.0098208] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 04/30/2014] [Indexed: 01/20/2023] Open
Abstract
Understanding the molecular mechanisms of oral carcinogenesis will yield important advances in diagnostics, prognostics, effective treatment, and outcome of oral cancer. Hence, in this study we have investigated the proteomic and peptidomic profiles by combining an orthotopic murine model of oral squamous cell carcinoma (OSCC), mass spectrometry-based proteomics and biological network analysis. Our results indicated the up-regulation of proteins involved in actin cytoskeleton organization and cell-cell junction assembly events and their expression was validated in human OSCC tissues. In addition, the functional relevance of talin-1 in OSCC adhesion, migration and invasion was demonstrated. Taken together, this study identified specific processes deregulated in oral cancer and provided novel refined OSCC-targeting molecules.
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Affiliation(s)
- Daniela C. Granato
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, Brazil
| | - Mariana R. Zanetti
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, Brazil
| | - Rebeca Kawahara
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, Brazil
| | - Sami Yokoo
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, Brazil
| | - Romênia R. Domingues
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, Brazil
| | - Annelize Z. Aragão
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, Brazil
| | - Michelle Agostini
- Faculdade de Odontologia de Piracicaba, Universidade Estadual de Campinas, UNICAMP, Piracicaba, Brazil
- Faculdade de Odontologia, Universidade Federal do Rio de Janeiro, UFRJ, Rio de Janeiro, Brazil
| | - Marcelo F. Carazzolle
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, Brazil
| | - Ramon O. Vidal
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, Brazil
| | - Isadora L. Flores
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, Brazil
- Faculdade de Odontologia de Piracicaba, Universidade Estadual de Campinas, UNICAMP, Piracicaba, Brazil
| | | | - Nilva K. Cervigne
- Faculdade de Odontologia de Piracicaba, Universidade Estadual de Campinas, UNICAMP, Piracicaba, Brazil
| | - Alan R. S. Silva
- Faculdade de Odontologia de Piracicaba, Universidade Estadual de Campinas, UNICAMP, Piracicaba, Brazil
| | - Ricardo D. Coletta
- Faculdade de Odontologia de Piracicaba, Universidade Estadual de Campinas, UNICAMP, Piracicaba, Brazil
| | - Edgard Graner
- Faculdade de Odontologia de Piracicaba, Universidade Estadual de Campinas, UNICAMP, Piracicaba, Brazil
| | - Nicholas E. Sherman
- W. M. Keck Biomedical Mass Spectrometry Lab. University of Virginia, Charlottesville, Virginia, United States of America
| | - Adriana F. Paes Leme
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, Brazil
- * E-mail:
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In-depth proteomic delineation of the colorectal cancer exoproteome: Mechanistic insight and identification of potential biomarkers. J Proteomics 2014; 103:121-36. [DOI: 10.1016/j.jprot.2014.03.018] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 03/07/2014] [Accepted: 03/18/2014] [Indexed: 12/30/2022]
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Hamson EJ, Keane FM, Tholen S, Schilling O, Gorrell MD. Understanding fibroblast activation protein (FAP): Substrates, activities, expression and targeting for cancer therapy. Proteomics Clin Appl 2014; 8:454-63. [DOI: 10.1002/prca.201300095] [Citation(s) in RCA: 199] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 10/16/2013] [Indexed: 11/08/2022]
Affiliation(s)
- Elizabeth J. Hamson
- Molecular Hepatology; Centenary Institute and Sydney Medical School; University of Sydney; Sydney Australia
| | - Fiona M. Keane
- Molecular Hepatology; Centenary Institute and Sydney Medical School; University of Sydney; Sydney Australia
| | - Stefan Tholen
- Institute of Molecular Medicine and Cell Research; University of Freiburg; Freiburg Germany
- Faculty of Biology; University of Freiburg; Freiburg Germany
| | - Oliver Schilling
- Faculty of Biology; University of Freiburg; Freiburg Germany
- BIOSS Centre for Biological Signaling Studies; University of Freiburg; Freiburg Germany
| | - Mark D. Gorrell
- Molecular Hepatology; Centenary Institute and Sydney Medical School; University of Sydney; Sydney Australia
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Plasman K, Maurer-Stroh S, Gevaert K, Van Damme P. Holistic View on the Extended Substrate Specificities of Orthologous Granzymes. J Proteome Res 2014; 13:1785-93. [DOI: 10.1021/pr401104b] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Kim Plasman
- Department
of Medical Protein Research, VIB, B-9000 Ghent, Belgium
- Department
of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Sebastian Maurer-Stroh
- Bioinformatics
Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore 138671
- School
of Biological Sciences (SBS), Nanyang Technological University (NTU), Singapore 637551
| | - Kris Gevaert
- Department
of Medical Protein Research, VIB, B-9000 Ghent, Belgium
- Department
of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Petra Van Damme
- Department
of Medical Protein Research, VIB, B-9000 Ghent, Belgium
- Department
of Biochemistry, Ghent University, B-9000 Ghent, Belgium
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Ferraz Franco C, Santos R, Varela Coelho A. Proteolytic events are relevant cellular responses during nervous system regeneration of the starfish Marthasterias glacialis. J Proteomics 2014; 99:1-25. [DOI: 10.1016/j.jprot.2013.12.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Revised: 12/03/2013] [Accepted: 12/09/2013] [Indexed: 01/12/2023]
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Dickey SW, Baker RP, Cho S, Urban S. Proteolysis inside the membrane is a rate-governed reaction not driven by substrate affinity. Cell 2014; 155:1270-81. [PMID: 24315097 DOI: 10.1016/j.cell.2013.10.053] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Revised: 08/04/2013] [Accepted: 10/28/2013] [Indexed: 10/25/2022]
Abstract
Enzymatic cleavage of transmembrane anchors to release proteins from the membrane controls diverse signaling pathways and is implicated in more than a dozen diseases. How catalysis works within the viscous, water-excluding, two-dimensional membrane is unknown. We developed an inducible reconstitution system to interrogate rhomboid proteolysis quantitatively within the membrane in real time. Remarkably, rhomboid proteases displayed no physiological affinity for substrates (K(d) ~190 μM/0.1 mol%). Instead, ~10,000-fold differences in proteolytic efficiency with substrate mutants and diverse rhomboid proteases were reflected in k(cat) values alone. Analysis of gate-open mutant and solvent isotope effects revealed that substrate gating, not hydrolysis, is rate limiting. Ultimately, a single proteolytic event within the membrane normally takes minutes. Rhomboid intramembrane proteolysis is thus a slow, kinetically controlled reaction not driven by transmembrane protein-protein affinity. These properties are unlike those of other studied proteases or membrane proteins but are strikingly reminiscent of one subset of DNA-repair enzymes, raising important mechanistic and drug-design implications.
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Affiliation(s)
- Seth W Dickey
- Howard Hughes Medical Institute, Department of Molecular Biology & Genetics, Johns Hopkins University School of Medicine, Room 507 PCTB, 725 North Wolfe Street, Baltimore, MD 21205, USA
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Amado F, Lobo MJC, Domingues P, Duarte JA, Vitorino R. Salivary peptidomics. Expert Rev Proteomics 2014; 7:709-21. [DOI: 10.1586/epr.10.48] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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50
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Pham VC, Anania VG, Phung QT, Lill JR. Complementary methods for the identification of substrates of proteolysis. Methods Enzymol 2014; 544:359-80. [PMID: 24974297 DOI: 10.1016/b978-0-12-417158-9.00014-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Proteolysis describes the cleavage of proteins into smaller components, which in vivo occurs typically to either activate or impair the functionality of cellular proteins. Proteolysis can occur during cellular homeostasis or can be induced due to external stress stimuli such as heat, biological or chemical insult, and is mediated by the activity of cellular enzymes, namely, proteases. Proteolytic cleavage of proteins can influence protein activation by exposing an active site or disrupting inhibitor binding. Conversely, proteolytic cleavage of many proteins has also been shown to lead to protein degradation resulting in inactivation of the substrate. Thousands of proteolytic events are known to take place in regulated cellular processes such as apoptosis and pyroptosis, however, their individual contribution to these processes remains poorly understood. Additionally, many cellular homeostatic processes are regulated by proteolytic events, however, in some cases, few proteolytic substrates have been identified. To gain further insight into the mechanism of action of these cellular processes, and to characterize biomarkers of cell death and other pathological indications, it is imperative to utilize a complete arsenal of tools for studying proteolysis events in vivo and in vitro. In this chapter, we focus on alternative methodologies to N-terminomics for profiling substrates of proteolysis and describe an additional suite of tools including orthogonal biophysical separation techniques such as COFRADIC or GASSP, and affinity capture tools that can enrich for newly formed C-termini (C-terminomics) generated as a result of caspase-mediated proteolysis.
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Affiliation(s)
- Victoria C Pham
- Department of Protein Chemistry, Genentech Inc., South San Francisco, California, USA
| | - Veronica G Anania
- Department of Protein Chemistry, Genentech Inc., South San Francisco, California, USA
| | - Qui T Phung
- Department of Protein Chemistry, Genentech Inc., South San Francisco, California, USA
| | - Jennie R Lill
- Department of Protein Chemistry, Genentech Inc., South San Francisco, California, USA.
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