1
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Zdravkova K, Mijanovic O, Brankovic A, Ilicheva PM, Jakovleva A, Karanovic J, Pualic M, Pualic D, Rubel AA, Savvateeva LV, Parodi A, Zamyatnin AA. Unveiling the Roles of Cysteine Proteinases F and W: From Structure to Pathological Implications and Therapeutic Targets. Cells 2024; 13:917. [PMID: 38891048 PMCID: PMC11171618 DOI: 10.3390/cells13110917] [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: 04/06/2024] [Revised: 05/22/2024] [Accepted: 05/23/2024] [Indexed: 06/20/2024] Open
Abstract
Cysteine cathepsins F and W are members of the papain-like cysteine protease family, which have distinct structural features and functional roles in various physiological and pathological processes. This review provides a comprehensive overview of the current understanding of the structure, biological functions, and pathological implications of cathepsins F and W. Beginning with an introduction to these proteases, we delve into their structural characteristics and elucidate their unique features that dictate their enzymatic activities and substrate specificity. We also explore the intricate involvement of cathepsins F and W in malignancies, highlighting their role as potential biomarkers and therapeutic targets in cancer progression. Furthermore, we discuss the emerging roles of these enzymes in immune response modulation and neurological disorders, shedding light on their implications in autoimmune and neurodegenerative diseases. Finally, we review the landscape of inhibitors targeting these proteases, highlighting their therapeutic potential and challenges in clinical translation. This review brings together the diverse facets of cysteine cathepsins F and W, providing insights into their roles in health and disease and guiding future investigations for therapeutic advances.
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Affiliation(s)
- Kristina Zdravkova
- AD Alkaloid Skopje, Boulevard Alexander the Great 12, 1000 Skopje, North Macedonia;
| | - Olja Mijanovic
- Dia-M, LCC, 7 b.3 Magadanskaya Str., 129345 Moscow, Russia;
| | - Ana Brankovic
- Department of Forensic Sciences, Faculty of Forensic Sciences and Engineering, University of Criminal Investigation and Police Studies, Cara Dusana 196, 11000 Belgrade, Serbia;
| | - Polina M. Ilicheva
- Institute of Chemistry, Saratov State University, Astrakhanskaya Street 83, 410012 Saratov, Russia;
| | | | - Jelena Karanovic
- Laboratory for Molecular Biology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444A, 11000 Belgrade, Serbia;
| | - Milena Pualic
- Institute Cardiovascular Diseases Dedinje, Heroja Milana Tepica 1, 11000 Belgrade, Serbia;
| | - Dusan Pualic
- Military Medical Academy, Crnotravska 17, 11000 Belgrade, Serbia;
| | - Aleksandr A. Rubel
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia;
| | - Lyudmila V. Savvateeva
- Institute of Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, 119991 Moscow, Russia;
| | - Alessandro Parodi
- Research Center for Translational Medicine, Sirius University of Science and Technology, 354340 Sochi, Russia;
| | - Andrey A. Zamyatnin
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
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2
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Falke S, Lieske J, Herrmann A, Loboda J, Karničar K, Günther S, Reinke PYA, Ewert W, Usenik A, Lindič N, Sekirnik A, Dretnik K, Tsuge H, Turk V, Chapman HN, Hinrichs W, Ebert G, Turk D, Meents A. Structural Elucidation and Antiviral Activity of Covalent Cathepsin L Inhibitors. J Med Chem 2024; 67:7048-7067. [PMID: 38630165 PMCID: PMC11089505 DOI: 10.1021/acs.jmedchem.3c02351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 03/22/2024] [Accepted: 03/28/2024] [Indexed: 05/15/2024]
Abstract
Emerging RNA viruses, including SARS-CoV-2, continue to be a major threat. Cell entry of SARS-CoV-2 particles via the endosomal pathway involves cysteine cathepsins. Due to ubiquitous expression, cathepsin L (CatL) is considered a promising drug target in the context of different viral and lysosome-related diseases. We characterized the anti-SARS-CoV-2 activity of a set of carbonyl- and succinyl epoxide-based inhibitors, which were previously identified as inhibitors of cathepsins or related cysteine proteases. Calpain inhibitor XII, MG-101, and CatL inhibitor IV possess antiviral activity in the very low nanomolar EC50 range in Vero E6 cells and inhibit CatL in the picomolar Ki range. We show a relevant off-target effect of CatL inhibition by the coronavirus main protease α-ketoamide inhibitor 13b. Crystal structures of CatL in complex with 14 compounds at resolutions better than 2 Å present a solid basis for structure-guided understanding and optimization of CatL inhibitors toward protease drug development.
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Affiliation(s)
- Sven Falke
- Center
for Free-Electron Laser Science CFEL, Deutsches
Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Julia Lieske
- Center
for Free-Electron Laser Science CFEL, Deutsches
Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Alexander Herrmann
- Institute
of Virology, Helmholtz Munich, Ingolstädter Landstraße 1, 85764 Neuherberg, Munich, Germany
| | - Jure Loboda
- Department
of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
| | - Katarina Karničar
- Department
of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
- Centre
of Excellence for Integrated Approaches in Chemistry and Biology of
Proteins, Jamova 39, 1000 Ljubljana, Slovenia
| | - Sebastian Günther
- Center
for Free-Electron Laser Science CFEL, Deutsches
Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Patrick Y. A. Reinke
- Center
for Free-Electron Laser Science CFEL, Deutsches
Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Wiebke Ewert
- Center
for Free-Electron Laser Science CFEL, Deutsches
Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Aleksandra Usenik
- Department
of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
- Centre
of Excellence for Integrated Approaches in Chemistry and Biology of
Proteins, Jamova 39, 1000 Ljubljana, Slovenia
| | - Nataša Lindič
- Department
of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
| | - Andreja Sekirnik
- Department
of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
| | - Klemen Dretnik
- Department
of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
- The
Jožef Stefan International Postgraduate School, Jamova cesta 39, 1000 Ljubljana, Slovenia
| | - Hideaki Tsuge
- Faculty of
Life Sciences, Kyoto Sangyo University, Kyoto 603-8555, Japan
| | - Vito Turk
- Department
of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
| | - Henry N. Chapman
- Center
for Free-Electron Laser Science CFEL, Deutsches
Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
- Hamburg
Centre for Ultrafast Imaging, Universität
Hamburg, Luruper Chaussee
149, 22761 Hamburg, Germany
- Department
of Physics, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Winfried Hinrichs
- Institute
of Biochemistry, Universität Greifswald, Felix-Hausdorff-Str. 4, 17489 Greifswald, Germany
| | - Gregor Ebert
- Institute
of Virology, Helmholtz Munich, Ingolstädter Landstraße 1, 85764 Neuherberg, Munich, Germany
- Institute
of Virology, Technical University of Munich, Trogerstraße 30, 81675 Munich, Germany
| | - Dušan Turk
- Department
of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
- Centre
of Excellence for Integrated Approaches in Chemistry and Biology of
Proteins, Jamova 39, 1000 Ljubljana, Slovenia
| | - Alke Meents
- Center
for Free-Electron Laser Science CFEL, Deutsches
Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
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3
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Grozdanić M, Sobotič B, Biasizzo M, Sever T, Vidmar R, Vizovišek M, Turk B, Fonović M. Cathepsin L-mediated EGFR cleavage affects intracellular signalling pathways in cancer. Biol Chem 2024; 405:283-296. [PMID: 37889671 DOI: 10.1515/hsz-2023-0213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 10/12/2023] [Indexed: 10/29/2023]
Abstract
Proteolytic activity in the tumour microenvironment is an important factor in cancer development since it can also affect intracellular signalling pathways via positive feedback loops that result in either increased tumour growth or resistance to anticancer mechanisms. In this study, we demonstrated extracellular cathepsin L-mediated cleavage of epidermal growth factor receptor (EGFR) and identified the cleavage site in the extracellular domain after R224. To further evaluate the relevance of this cleavage, we cloned and expressed a truncated version of EGFR, starting at G225, in HeLa cells. We confirmed the constitutive activation of the truncated protein in the absence of ligand binding and determined possible changes in intracellular signalling. Furthermore, we determined the effect of truncated EGFR protein expression on HeLa cell viability and response to the EGFR inhibitors, tyrosine kinase inhibitor (TKI) erlotinib and monoclonal antibody (mAb) cetuximab. Our data reveal the nuclear localization and phosphorylation of EGFR and signal trancducer and activator of transcription 3 (STAT3) in cells that express the truncated EGFR protein and suggest that these phenomena cause resistance to EGFR inhibitors.
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Affiliation(s)
- Marija Grozdanić
- Department of Biochemistry, Molecular and Structural Biology, Jozef Stefan Institute, Jamova cesta 39, SI-1000 Ljubljana, Slovenia
- International Postgraduate School Jožef Stefan, Jamova cesta 39, SI-1000 Ljubljana, Slovenia
| | - Barbara Sobotič
- Kymab Ltd, The Bennet Building (B930), Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Monika Biasizzo
- Department of Biochemistry, Molecular and Structural Biology, Jozef Stefan Institute, Jamova cesta 39, SI-1000 Ljubljana, Slovenia
- International Postgraduate School Jožef Stefan, Jamova cesta 39, SI-1000 Ljubljana, Slovenia
| | - Tilen Sever
- Department of Biochemistry, Molecular and Structural Biology, Jozef Stefan Institute, Jamova cesta 39, SI-1000 Ljubljana, Slovenia
- International Postgraduate School Jožef Stefan, Jamova cesta 39, SI-1000 Ljubljana, Slovenia
| | - Robert Vidmar
- Department of Biochemistry, Molecular and Structural Biology, Jozef Stefan Institute, Jamova cesta 39, SI-1000 Ljubljana, Slovenia
| | - Matej Vizovišek
- Department of Biochemistry, Molecular and Structural Biology, Jozef Stefan Institute, Jamova cesta 39, SI-1000 Ljubljana, Slovenia
| | - Boris Turk
- Department of Biochemistry, Molecular and Structural Biology, Jozef Stefan Institute, Jamova cesta 39, SI-1000 Ljubljana, Slovenia
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia
| | - Marko Fonović
- Department of Biochemistry, Molecular and Structural Biology, Jozef Stefan Institute, Jamova cesta 39, SI-1000 Ljubljana, Slovenia
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4
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Liu J, Zhang W, Wang Z, Wang Y, Li T, Wang Y, Ding J, Ning B. Cathepsin V is correlated with the prognosis and tumor microenvironment in liver cancer. Mol Carcinog 2024; 63:400-416. [PMID: 38051285 DOI: 10.1002/mc.23660] [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: 01/01/2023] [Revised: 10/28/2023] [Accepted: 11/07/2023] [Indexed: 12/07/2023]
Abstract
Recent studies have shown that high cell cycle activity negatively correlates with antitumor immunity in certain cancer types. However, a similar correlation has not been proven in liver cancer. We downloaded transcriptomic profiles of the cancer genome atlas-liver hepatocellular carcinoma (TCGA-LIHC) and assessed the cell cycle distribution of samples using single sample gene set enrichment analysis (ssGSEA), termed the cell cycle score (CCS). We obtained cell cycle-related differentially expressed prognostic genes and identified CENPA, CDC20, and CTSV using LASSO regression. We studied the effect of CTSV on clinical features and immune alterations in liver cancer based on TCGA-LIHC data. In vitro and in vivo experiments were performed to validate the role of CTSV in liver cancer using liver cancer cell lines and tissues. We found that the CCS closely correlated with the clinical features and prognosis of patients in TCGA-LIHC. Analysis of differentially expressed genes (DEGs), univariate Cox regression, and least absolute shrinkage and selection operator (LASSO) regression identified cathepsin V (CTSV) with prognostic significance in LIHC. Importantly, single-gene survival analysis of CTSV using microarray and sequencing data indicated that high levels of CTSV expression correlated with an unfavorable prognosis in various cancers. Gene set enrichment analysis revealed that high CTSV expression closely correlated with decreased expression of metabolic genes and increased expression of cell cycle genes. Furthermore, difference and correlation analyses of the relationship between CTSV expression and immune infiltrates, determined using CIBERSORT and TIMER algorithms, revealed that CTSV expression correlated with macrophages and CD4+ T cells. In vitro and in vivo experiments revealed that knockdown of CTSV inhibited liver cancer cells proliferation. Immunohistochemical staining showed that high CTSV expression correlated with macrophage infiltration in liver cancer tissues, predicted a poor prognosis, and is associated with the effectiveness of hepatocellular carcinoma treatment. In couclusion, CTSV is a novel cell cycle-associated gene with clinical significance in HCC.
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Affiliation(s)
- Junyu Liu
- Center for Translational Medicine, Clinical Cancer Institute, Naval Military Medical University, Shanghai, China
- National Center for Liver Cancer, Third Affiliated Hospital of Naval Military Medical University, Shanghai, China
| | - Wen Zhang
- Center for Translational Medicine, Clinical Cancer Institute, Naval Military Medical University, Shanghai, China
| | - Zhijie Wang
- Center for Translational Medicine, Clinical Cancer Institute, Naval Military Medical University, Shanghai, China
| | - Yichuan Wang
- Center for Translational Medicine, Clinical Cancer Institute, Naval Military Medical University, Shanghai, China
| | - Tianxing Li
- Department of Gastroenterology, Changzheng Hospital, The Second Military Medical University, Shanghai, China
| | - Yaping Wang
- Center for Translational Medicine, Clinical Cancer Institute, Naval Military Medical University, Shanghai, China
| | - Jin Ding
- Center for Translational Medicine, Clinical Cancer Institute, Naval Military Medical University, Shanghai, China
- National Center for Liver Cancer, Third Affiliated Hospital of Naval Military Medical University, Shanghai, China
| | - Beifang Ning
- Department of Gastroenterology, Changzheng Hospital, The Second Military Medical University, Shanghai, China
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5
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Matoušková Z, Orsághová K, Srb P, Pytelková J, Kukačka Z, Buša M, Hajdušek O, Šíma R, Fábry M, Novák P, Horn M, Kopáček P, Mareš M. An Unusual Two-Domain Thyropin from Tick Saliva: NMR Solution Structure and Highly Selective Inhibition of Cysteine Cathepsins Modulated by Glycosaminoglycans. Int J Mol Sci 2024; 25:2240. [PMID: 38396918 PMCID: PMC10889554 DOI: 10.3390/ijms25042240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 02/02/2024] [Accepted: 02/10/2024] [Indexed: 02/25/2024] Open
Abstract
The structure and biochemical properties of protease inhibitors from the thyropin family are poorly understood in parasites and pathogens. Here, we introduce a novel family member, Ir-thyropin (IrThy), which is secreted in the saliva of Ixodes ricinus ticks, vectors of Lyme borreliosis and tick-borne encephalitis. The IrThy molecule consists of two consecutive thyroglobulin type-1 (Tg1) domains with an unusual disulfide pattern. Recombinant IrThy was found to inhibit human host-derived cathepsin proteases with a high specificity for cathepsins V, K, and L among a wide range of screened cathepsins exhibiting diverse endo- and exopeptidase activities. Both Tg1 domains displayed inhibitory activities, but with distinct specificity profiles. We determined the spatial structure of one of the Tg1 domains by solution NMR spectroscopy and described its reactive center to elucidate the unique inhibitory specificity. Furthermore, we found that the inhibitory potency of IrThy was modulated in a complex manner by various glycosaminoglycans from host tissues. IrThy was additionally regulated by pH and proteolytic degradation. This study provides a comprehensive structure-function characterization of IrThy-the first investigated thyropin of parasite origin-and suggests its potential role in host-parasite interactions at the tick bite site.
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Affiliation(s)
- Zuzana Matoušková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo n. 2, 16610 Praha, Czech Republic; (Z.M.); (K.O.); (M.B.); (M.F.); (M.H.)
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 8, 12800 Praha, Czech Republic
| | - Katarína Orsághová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo n. 2, 16610 Praha, Czech Republic; (Z.M.); (K.O.); (M.B.); (M.F.); (M.H.)
- First Faculty of Medicine, Charles University, Katerinska 32, 12108 Praha, Czech Republic
| | - Pavel Srb
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo n. 2, 16610 Praha, Czech Republic; (Z.M.); (K.O.); (M.B.); (M.F.); (M.H.)
| | - Jana Pytelková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo n. 2, 16610 Praha, Czech Republic; (Z.M.); (K.O.); (M.B.); (M.F.); (M.H.)
| | - Zdeněk Kukačka
- Institute of Microbiology, Czech Academy of Sciences, Prumyslova 595, 25250 Vestec, Czech Republic
| | - Michal Buša
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo n. 2, 16610 Praha, Czech Republic; (Z.M.); (K.O.); (M.B.); (M.F.); (M.H.)
| | - Ondřej Hajdušek
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branisovska 31, 37005 Ceske Budejovice, Czech Republic
| | - Radek Šíma
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branisovska 31, 37005 Ceske Budejovice, Czech Republic
- Biopticka Laborator, Mikulasske Namesti 4, 32600 Plzen, Czech Republic
| | - Milan Fábry
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo n. 2, 16610 Praha, Czech Republic; (Z.M.); (K.O.); (M.B.); (M.F.); (M.H.)
| | - Petr Novák
- Institute of Microbiology, Czech Academy of Sciences, Prumyslova 595, 25250 Vestec, Czech Republic
| | - Martin Horn
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo n. 2, 16610 Praha, Czech Republic; (Z.M.); (K.O.); (M.B.); (M.F.); (M.H.)
| | - Petr Kopáček
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branisovska 31, 37005 Ceske Budejovice, Czech Republic
| | - Michael Mareš
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo n. 2, 16610 Praha, Czech Republic; (Z.M.); (K.O.); (M.B.); (M.F.); (M.H.)
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6
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Reinke PYA, de Souza EE, Günther S, Falke S, Lieske J, Ewert W, Loboda J, Herrmann A, Rahmani Mashhour A, Karničar K, Usenik A, Lindič N, Sekirnik A, Botosso VF, Santelli GMM, Kapronezai J, de Araújo MV, Silva-Pereira TT, Filho AFDS, Tavares MS, Flórez-Álvarez L, de Oliveira DBL, Durigon EL, Giaretta PR, Heinemann MB, Hauser M, Seychell B, Böhler H, Rut W, Drag M, Beck T, Cox R, Chapman HN, Betzel C, Brehm W, Hinrichs W, Ebert G, Latham SL, Guimarães AMDS, Turk D, Wrenger C, Meents A. Calpeptin is a potent cathepsin inhibitor and drug candidate for SARS-CoV-2 infections. Commun Biol 2023; 6:1058. [PMID: 37853179 PMCID: PMC10584882 DOI: 10.1038/s42003-023-05317-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 09/01/2023] [Indexed: 10/20/2023] Open
Abstract
Several drug screening campaigns identified Calpeptin as a drug candidate against SARS-CoV-2. Initially reported to target the viral main protease (Mpro), its moderate activity in Mpro inhibition assays hints at a second target. Indeed, we show that Calpeptin is an extremely potent cysteine cathepsin inhibitor, a finding additionally supported by X-ray crystallography. Cell infection assays proved Calpeptin's efficacy against SARS-CoV-2. Treatment of SARS-CoV-2-infected Golden Syrian hamsters with sulfonated Calpeptin at a dose of 1 mg/kg body weight reduces the viral load in the trachea. Despite a higher risk of side effects, an intrinsic advantage in targeting host proteins is their mutational stability in contrast to highly mutable viral targets. Here we show that the inhibition of cathepsins, a protein family of the host organism, by calpeptin is a promising approach for the treatment of SARS-CoV-2 and potentially other viral infections.
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Affiliation(s)
- Patrick Y A Reinke
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Edmarcia Elisa de Souza
- Department of Parasitology, Institute of Biomedical Sciences at the University of São Paulo, São Paulo, Brazil
| | - Sebastian Günther
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Sven Falke
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Julia Lieske
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Wiebke Ewert
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Jure Loboda
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000, Ljubljana, Slovenia
- Jožef Stefan International Postgraduate School, Jamova 39, Ljubljana, Slovenia
| | | | - Aida Rahmani Mashhour
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Katarina Karničar
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000, Ljubljana, Slovenia
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova 39, 1000, Ljubljana, Slovenia
| | - Aleksandra Usenik
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000, Ljubljana, Slovenia
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova 39, 1000, Ljubljana, Slovenia
| | - Nataša Lindič
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000, Ljubljana, Slovenia
| | - Andreja Sekirnik
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000, Ljubljana, Slovenia
| | - Viviane Fongaro Botosso
- Virology Laboratory, Center of Development and Innovation, Butantan Institute, São Paulo, Brazil
| | - Gláucia Maria Machado Santelli
- Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Josana Kapronezai
- Virology Laboratory, Center of Development and Innovation, Butantan Institute, São Paulo, Brazil
| | - Marcelo Valdemir de Araújo
- Virology Laboratory, Center of Development and Innovation, Butantan Institute, São Paulo, Brazil
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Taiana Tainá Silva-Pereira
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
- Department of Preventive Veterinary Medicine and Animal Health, College of Veterinary Medicine, University of São Paulo, São Paulo, Brazil
| | | | - Mariana Silva Tavares
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Lizdany Flórez-Álvarez
- Department of Parasitology, Institute of Biomedical Sciences at the University of São Paulo, São Paulo, Brazil
| | | | - Edison Luiz Durigon
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Paula Roberta Giaretta
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, 4474 TAMU, School Station, TX, USA
| | - Marcos Bryan Heinemann
- Department of Preventive Veterinary Medicine and Animal Health, College of Veterinary Medicine, University of São Paulo, São Paulo, Brazil
| | - Maurice Hauser
- Institute for Organic Chemistry and BMWZ, Leibniz University of Hannover, Schneiderberg 38, 30167, Hannover, Germany
| | - Brandon Seychell
- Department of Chemistry, Institute of Physical Chemistry, Universität Hamburg, Grindelallee 117, 20146, Hamburg, Germany
| | - Hendrik Böhler
- Department of Chemistry, Institute of Physical Chemistry, Universität Hamburg, Grindelallee 117, 20146, Hamburg, Germany
| | - Wioletta Rut
- Department of Chemical Biology and Bioimaging, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland
| | - Marcin Drag
- Department of Chemical Biology and Bioimaging, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland
| | - Tobias Beck
- Department of Chemistry, Institute of Physical Chemistry, Universität Hamburg, Grindelallee 117, 20146, Hamburg, Germany
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Russell Cox
- Institute for Organic Chemistry and BMWZ, Leibniz University of Hannover, Schneiderberg 38, 30167, Hannover, Germany
| | - Henry N Chapman
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Christian Betzel
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Department of Chemistry, Institute of Biochemistry and Molecular Biology and Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, Universität Hamburg, 22607, Hamburg, Germany
| | - Wolfgang Brehm
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Winfried Hinrichs
- Universität Greifswald, Institute of Biochemistry, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Gregor Ebert
- Institute of Virology, Helmholtz Munich, Munich, Germany
- Institute of Virology, Technical University of Munich, Munich, Germany
| | - Sharissa L Latham
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, NSW, Australia
- St Vincent's Hospital Clinical School, UNSW, Sydney, NSW, Australia
| | - Ana Marcia de Sá Guimarães
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Dusan Turk
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000, Ljubljana, Slovenia.
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova 39, 1000, Ljubljana, Slovenia.
| | - Carsten Wrenger
- Department of Parasitology, Institute of Biomedical Sciences at the University of São Paulo, São Paulo, Brazil.
| | - Alke Meents
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany.
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7
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Tušar L, Loboda J, Impens F, Sosnowski P, Van Quickelberghe E, Vidmar R, Demol H, Sedeyn K, Saelens X, Vizovišek M, Mihelič M, Fonović M, Horvat J, Kosec G, Turk B, Gevaert K, Turk D. Proteomic data and structure analysis combined reveal interplay of structural rigidity and flexibility on selectivity of cysteine cathepsins. Commun Biol 2023; 6:450. [PMID: 37095140 PMCID: PMC10124925 DOI: 10.1038/s42003-023-04772-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 03/28/2023] [Indexed: 04/26/2023] Open
Abstract
Addressing the elusive specificity of cysteine cathepsins, which in contrast to caspases and trypsin-like proteases lack strict specificity determining P1 pocket, calls for innovative approaches. Proteomic analysis of cell lysates with human cathepsins K, V, B, L, S, and F identified 30,000 cleavage sites, which we analyzed by software platform SAPS-ESI (Statistical Approach to Peptidyl Substrate-Enzyme Specific Interactions). SAPS-ESI is used to generate clusters and training sets for support vector machine learning. Cleavage site predictions on the SARS-CoV-2 S protein, confirmed experimentally, expose the most probable first cut under physiological conditions and suggested furin-like behavior of cathepsins. Crystal structure analysis of representative peptides in complex with cathepsin V reveals rigid and flexible sites consistent with analysis of proteomics data by SAPS-ESI that correspond to positions with heterogeneous and homogeneous distribution of residues. Thereby support for design of selective cleavable linkers of drug conjugates and drug discovery studies is provided.
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Affiliation(s)
- Livija Tušar
- Jožef Stefan Institute, Department of Biochemistry and Molecular and Structural Biology, Jamova cesta 39, 1000, Ljubljana, Slovenia
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins (CIPKeBiP), Jamova cesta 39, 1000, Ljubljana, Slovenia
| | - Jure Loboda
- Jožef Stefan Institute, Department of Biochemistry and Molecular and Structural Biology, Jamova cesta 39, 1000, Ljubljana, Slovenia
- The Jožef Stefan International Postgraduate School, Jamova cesta 39, 1000, Ljubljana, Slovenia
| | - Francis Impens
- VIB-UGent Center for Medical Biotechnology and UGent Department of Biomolecular Medicine, Technologiepark-Zwijnaarde 75, 9052, Ghent, Belgium
| | - Piotr Sosnowski
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins (CIPKeBiP), Jamova cesta 39, 1000, Ljubljana, Slovenia
| | - Emmy Van Quickelberghe
- VIB-UGent Center for Medical Biotechnology and UGent Department of Biomolecular Medicine, Technologiepark-Zwijnaarde 75, 9052, Ghent, Belgium
| | - Robert Vidmar
- Jožef Stefan Institute, Department of Biochemistry and Molecular and Structural Biology, Jamova cesta 39, 1000, Ljubljana, Slovenia
| | - Hans Demol
- VIB-UGent Center for Medical Biotechnology and UGent Department of Biomolecular Medicine, Technologiepark-Zwijnaarde 75, 9052, Ghent, Belgium
| | - Koen Sedeyn
- VIB-UGent Center for Medical Biotechnology and, Department for Biochemistry and Microbiology, Ghent University, 9052, Ghent, Belgium
| | - Xavier Saelens
- VIB-UGent Center for Medical Biotechnology and, Department for Biochemistry and Microbiology, Ghent University, 9052, Ghent, Belgium
| | - Matej Vizovišek
- Jožef Stefan Institute, Department of Biochemistry and Molecular and Structural Biology, Jamova cesta 39, 1000, Ljubljana, Slovenia
| | - Marko Mihelič
- Jožef Stefan Institute, Department of Biochemistry and Molecular and Structural Biology, Jamova cesta 39, 1000, Ljubljana, Slovenia
| | - Marko Fonović
- Jožef Stefan Institute, Department of Biochemistry and Molecular and Structural Biology, Jamova cesta 39, 1000, Ljubljana, Slovenia
| | - Jaka Horvat
- Acies Bio d.o.o., Tehnološki park 21, 1000, Ljubljana, Slovenia
| | - Gregor Kosec
- Acies Bio d.o.o., Tehnološki park 21, 1000, Ljubljana, Slovenia
| | - Boris Turk
- Jožef Stefan Institute, Department of Biochemistry and Molecular and Structural Biology, Jamova cesta 39, 1000, Ljubljana, Slovenia
- Faculty of Chemistry, University of Ljubljana, Večna pot 113, SI-1000, Ljubljana, Slovenia
| | - Kris Gevaert
- VIB-UGent Center for Medical Biotechnology and UGent Department of Biomolecular Medicine, Technologiepark-Zwijnaarde 75, 9052, Ghent, Belgium.
| | - Dušan Turk
- Jožef Stefan Institute, Department of Biochemistry and Molecular and Structural Biology, Jamova cesta 39, 1000, Ljubljana, Slovenia.
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins (CIPKeBiP), Jamova cesta 39, 1000, Ljubljana, Slovenia.
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8
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Janiszewski T, Kołt S, Ciastoń I, Vizovisek M, Poręba M, Turk B, Drąg M, Kozieł J, Kasperkiewicz P. Investigation of osteoclast cathepsin K activity in osteoclastogenesis and bone loss using a set of chemical reagents. Cell Chem Biol 2023; 30:159-174.e8. [PMID: 36696904 DOI: 10.1016/j.chembiol.2023.01.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 08/28/2022] [Accepted: 01/04/2023] [Indexed: 01/26/2023]
Abstract
Cathepsin K (CatK) is a lysosomal cysteine protease whose highest expression is found in osteoclasts, which are the cells responsible for bone resorption. Investigations of the functions and physiological relevance of CatK have often relied on antibody-related techniques, which makes studying its activity patterns a challenging task. Hence, we developed a set of chemical tools for the investigation of CatK activity. We show that our probe is a valuable tool for monitoring the proteolytic activation of CatK during osteoclast formation. Moreover, we demonstrate that our inhibitor of CatK impedes osteoclastogenesis and bone resorption and that CatK is stored in its active form in osteoclasts within their lysosomal compartment and mainly in the ruffled borders of osteoclasts. Given that our probe recognizes active CatK within living cells without exhibiting any observed cytotoxicity in the several models tested, we expect that it would be well suited to theranostic applications in CatK-related diseases.
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Affiliation(s)
- Tomasz Janiszewski
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Sonia Kołt
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Izabela Ciastoń
- Department of Microbiology, Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, ul. Gronostajowa 7, 30-387 Kraków, Poland
| | - Matej Vizovisek
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
| | - Marcin Poręba
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Boris Turk
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia; Faculty of Chemistry and Chemical Technology, University of Ljubljana, Vecna pot 113, 1000 Ljubljana, Slovenia
| | - Marcin Drąg
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Joanna Kozieł
- Department of Microbiology, Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, ul. Gronostajowa 7, 30-387 Kraków, Poland
| | - Paulina Kasperkiewicz
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland.
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9
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Sullivan GP, Davidovich P, Muñoz-Wolf N, Ward RW, Hernandez Santana YE, Clancy DM, Gorman A, Najda Z, Turk B, Walsh PT, Lavelle EC, Martin SJ. Myeloid cell-derived proteases produce a proinflammatory form of IL-37 that signals via IL-36 receptor engagement. Sci Immunol 2022; 7:eade5728. [PMID: 36525507 DOI: 10.1126/sciimmunol.ade5728] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Interleukin-1 (IL-1) family cytokines are key barrier cytokines that are typically expressed as inactive, or partially active, precursors that require proteolysis within their amino termini for activation. IL-37 is an enigmatic member of the IL-1 family that has been proposed to be activated by caspase-1 and to exert anti-inflammatory activity through engagement of the IL-18R and SIGIRR. However, here we show that the longest IL-37 isoform, IL-37b, exhibits robust proinflammatory activity upon amino-terminal proteolysis by neutrophil elastase or cathepsin S. In sharp contrast, caspase-1 failed to process or activate IL-37 at concentrations that robustly activated its canonical substrate, IL-1β. IL-37 and IL-36 exhibit high structural homology, and, consistent with this, a K53-truncated form of IL-37, mimicking the cathepsin S-processed form of this cytokine, was found to exert its proinflammatory effects via IL-36 receptor engagement and produced an inflammatory signature practically identical to IL-36. Administration of K53-truncated IL-37b intraperitoneally into wild-type mice also elicited an inflammatory response that was attenuated in IL-36R-/- animals. These data demonstrate that, in common with other IL-1 family members, mature IL-37 can also elicit proinflammatory effects upon processing by specific proteases.
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Affiliation(s)
- Graeme P Sullivan
- Molecular Cell Biology Laboratory, Department of Genetics, Smurfit Institute, Trinity College, Dublin 2, Ireland
| | - Pavel Davidovich
- Molecular Cell Biology Laboratory, Department of Genetics, Smurfit Institute, Trinity College, Dublin 2, Ireland
| | - Natalia Muñoz-Wolf
- Adjuvant Research Group, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College, Dublin 2, Ireland.,4National Children's Research Centre, CHI-Crumlin, Dublin, Ireland
| | - Ross W Ward
- Adjuvant Research Group, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College, Dublin 2, Ireland
| | | | - Danielle M Clancy
- Molecular Cell Biology Laboratory, Department of Genetics, Smurfit Institute, Trinity College, Dublin 2, Ireland
| | - Aoife Gorman
- Adjuvant Research Group, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College, Dublin 2, Ireland
| | - Zaneta Najda
- Molecular Cell Biology Laboratory, Department of Genetics, Smurfit Institute, Trinity College, Dublin 2, Ireland
| | - Boris Turk
- Department of Biochemistry, Molecular and Structural Biology, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Patrick T Walsh
- Department of Clinical Medicine, School of Medicine, Trinity College, Dublin 2, Ireland.,Department of Biochemistry, Molecular and Structural Biology, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Ed C Lavelle
- Adjuvant Research Group, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College, Dublin 2, Ireland
| | - Seamus J Martin
- Molecular Cell Biology Laboratory, Department of Genetics, Smurfit Institute, Trinity College, Dublin 2, Ireland
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10
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Lecaille F, Chazeirat T, Saidi A, Lalmanach G. Cathepsin V: Molecular characteristics and significance in health and disease. Mol Aspects Med 2022; 88:101086. [PMID: 35305807 DOI: 10.1016/j.mam.2022.101086] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 02/23/2022] [Accepted: 02/26/2022] [Indexed: 12/31/2022]
Abstract
Human cysteine cathepsins form a family of eleven proteases (B, C, F, H, K, L, O, S, V, W, X/Z) that play important roles in a considerable number of biological and pathophysiological processes. Among them, cathepsin V, also known as cathepsin L2, is a lysosomal enzyme, which is mainly expressed in cornea, thymus, heart, brain, and skin. Cathepsin V is a multifunctional endopeptidase that is involved in both the release of antigenic peptides and the maturation of MHC class II molecules and participates in the turnover of elastin fibrils as well in the cleavage of intra- and extra-cellular substrates. Moreover, there is increasing evidence that cathepsin V may contribute to the progression of diverse diseases, due to the dysregulation of its expression and/or its activity. For instance, increased expression of cathepsin V is closely correlated with malignancies (breast cancer, squamous cell carcinoma, or colorectal cancer) as well vascular disorders (atherosclerosis, aortic aneurysm, hypertension) being the most prominent examples. This review aims to shed light on current knowledge on molecular aspects of cathepsin V (genomic organization, protein structure, substrate specificity), its regulation by protein and non-protein inhibitors as well to summarize its expression (tissue and cellular distribution). Then the core biological and pathophysiological roles of cathepsin V will be depicted, raising the question of its interest as a valuable target that can open up pioneering therapeutic avenues.
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Affiliation(s)
- Fabien Lecaille
- Université de Tours, Tours, France; INSERM, UMR 1100, Centre d'Etude des Pathologies Respiratoires (CEPR), Team "Mécanismes protéolytiques dans l'inflammation", Tours, France.
| | - Thibault Chazeirat
- Université de Tours, Tours, France; INSERM, UMR 1100, Centre d'Etude des Pathologies Respiratoires (CEPR), Team "Mécanismes protéolytiques dans l'inflammation", Tours, France
| | - Ahlame Saidi
- Université de Tours, Tours, France; INSERM, UMR 1100, Centre d'Etude des Pathologies Respiratoires (CEPR), Team "Mécanismes protéolytiques dans l'inflammation", Tours, France
| | - Gilles Lalmanach
- Université de Tours, Tours, France; INSERM, UMR 1100, Centre d'Etude des Pathologies Respiratoires (CEPR), Team "Mécanismes protéolytiques dans l'inflammation", Tours, France.
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11
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Microglial CD74 Expression Is Regulated by TGFβ Signaling. Int J Mol Sci 2022; 23:ijms231810247. [PMID: 36142162 PMCID: PMC9499470 DOI: 10.3390/ijms231810247] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 08/31/2022] [Accepted: 09/02/2022] [Indexed: 11/17/2022] Open
Abstract
Simple Summary In the present study, we provided evidence that TGFβ signaling regulated the expression of the microglia activation marker CD74. Our data demonstrated that TGFβ1 inhibited LPS-induced upregulation of CD74. Moreover, inhibition of microglial TGFβ signaling in vitro and silencing of TGFβ signaling by deletion of Tgfbr2 in vivo resulted in marked upregulation of microglial CD74. Abstract Microglia play important roles during physiological and pathological situations in the CNS. Several reports have described the expression of Cd74 in disease-associated and aged microglia. Here, we demonstrated that TGFβ1 controled the expression of Cd74 in microglia in vitro and in vivo. Using BV2 cells, primary microglia cultures as well as Cx3cr1CreERT2:R26-YFP:Tgfbr2fl/fl in combination with qPCR, flow cytometry, and immunohistochemistry, we were able to provide evidence that TGFβ1 inhibited LPS-induced upregulation of Cd74 in microglia. Interestingly, TGFβ1 alone was able to mediate downregulation of CD74 in vitro. Moreover, silencing of TGFβ signaling in vivo resulted in marked upregulation of CD74, further underlining the importance of microglial TGFβ signaling during regulation of microglia activation. Taken together, our data indicated that CD74 is a marker for activated microglia and further demonstrated that microglial TGFβ signaling is important for regulation of Cd74 expression during microglia activation.
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12
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Abnormal global alternative RNA splicing in COVID-19 patients. PLoS Genet 2022; 18:e1010137. [PMID: 35421082 PMCID: PMC9089920 DOI: 10.1371/journal.pgen.1010137] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 05/10/2022] [Accepted: 03/08/2022] [Indexed: 12/25/2022] Open
Abstract
Viral infections can alter host transcriptomes by manipulating host splicing machinery. Despite intensive transcriptomic studies on SARS-CoV-2, a systematic analysis of alternative splicing (AS) in severe COVID-19 patients remains largely elusive. Here we integrated proteomic and transcriptomic sequencing data to study AS changes in COVID-19 patients. We discovered that RNA splicing is among the major down-regulated proteomic signatures in COVID-19 patients. The transcriptome analysis showed that SARS-CoV-2 infection induces widespread dysregulation of transcript usage and expression, affecting blood coagulation, neutrophil activation, and cytokine production. Notably, CD74 and LRRFIP1 had increased skipping of an exon in COVID-19 patients that disrupts a functional domain, which correlated with reduced antiviral immunity. Furthermore, the dysregulation of transcripts was strongly correlated with clinical severity of COVID-19, and splice-variants may contribute to unexpected therapeutic activity. In summary, our data highlight that a better understanding of the AS landscape may aid in COVID-19 diagnosis and therapy. Despite intensive studies on the transcriptional signatures of COVID-19 patients, how SARS-CoV-2 affects AS landscape and the contribution of AS to the pathogenesis of COVID-19 remain largely elusive. By profiling the lung transcriptome and lung proteome of nine patients who died of COVID-19 during the first wave of the pandemic in Wuhan, China, we obtained molecular insights into the AS of cellular transcripts upon SARS-CoV-2 infection. Interestingly, SARS-CoV-2 proteins directly engage host spliceosome to dysregulate essential steps of mature mRNA production and result in widespread dysregulation of cellular function. Taken together, our findings shed light on COVID-19 molecular mechanism and offer potential therapeutic targets for severe COVID-19 disease.
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13
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Zhao X, Chen D, Li X, Griffith L, Chang J, An P, Guo JT. Interferon Control of Human Coronavirus Infection and Viral Evasion: Mechanistic Insights and Implications for Antiviral Drug and Vaccine Development. J Mol Biol 2022; 434:167438. [PMID: 34990653 PMCID: PMC8721920 DOI: 10.1016/j.jmb.2021.167438] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 12/24/2021] [Accepted: 12/29/2021] [Indexed: 12/16/2022]
Abstract
Recognition of viral infections by various pattern recognition receptors (PRRs) activates an inflammatory cytokine response that inhibits viral replication and orchestrates the activation of adaptive immune responses to control the viral infection. The broadly active innate immune response puts a strong selective pressure on viruses and drives the selection of variants with increased capabilities to subvert the induction and function of antiviral cytokines. This revolutionary process dynamically shapes the host ranges, cell tropism and pathogenesis of viruses. Recent studies on the innate immune responses to the infection of human coronaviruses (HCoV), particularly SARS-CoV-2, revealed that HCoV infections can be sensed by endosomal toll-like receptors and/or cytoplasmic RIG-I-like receptors in various cell types. However, the profiles of inflammatory cytokines and transcriptome response induced by a specific HCoV are usually cell type specific and determined by the virus-specific mechanisms of subverting the induction and function of interferons and inflammatory cytokines as well as the genetic trait of the host genes of innate immune pathways. We review herein the recent literatures on the innate immune responses and their roles in the pathogenesis of HCoV infections with emphasis on the pathobiological roles and therapeutic effects of type I interferons in HCoV infections and their antiviral mechanisms. The knowledge on the mechanism of innate immune control of HCoV infections and viral evasions should facilitate the development of therapeutics for induction of immune resolution of HCoV infections and vaccines for efficient control of COVID-19 pandemics and other HCoV infections.
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Affiliation(s)
- Xuesen Zhao
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China; Beijing Institute of Infectious Diseases, Beijing 100015, China; National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China.
| | - Danying Chen
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China; Beijing Institute of Infectious Diseases, Beijing 100015, China; National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China
| | - Xinglin Li
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China; Beijing Institute of Infectious Diseases, Beijing 100015, China; National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China
| | - Lauren Griffith
- Baruch S. Blumberg Institute, Hepatitis B Foundation, 3805 Old Easton Road, Doylestown, PA 18902, USA
| | - Jinhong Chang
- Baruch S. Blumberg Institute, Hepatitis B Foundation, 3805 Old Easton Road, Doylestown, PA 18902, USA
| | - Ping An
- Basic Research Laboratory, National Cancer Institute, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Ju-Tao Guo
- Baruch S. Blumberg Institute, Hepatitis B Foundation, 3805 Old Easton Road, Doylestown, PA 18902, USA.
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14
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Clanchy FIL, Borghese F, Bystrom J, Balog A, Penn H, Taylor PC, Stone TW, Mageed RA, Williams RO. Disease status in human and experimental arthritis, and response to TNF blockade, is associated with MHC class II invariant chain (CD74) isoform expression. J Autoimmun 2022; 128:102810. [PMID: 35245865 DOI: 10.1016/j.jaut.2022.102810] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/15/2022] [Accepted: 02/19/2022] [Indexed: 11/25/2022]
Abstract
Splice variants of CD74 differentially modulate the activity of cathepsin L (CTSL). As CD74 and CTSL participate in the pathogenesis of inflammatory diseases such as rheumatoid arthritis (RA), we determined whether splice variants of CD74 could be biomarkers of disease activity. Gene expression was measured in mice with collagen-induced arthritis using quantitative PCR (qPCR). In vitro studies using murine macrophage/DC-lineage cells determined the relative influence of macrophage phenotype on isoform expression and the potential to produce CTSL in response to TNF. CD74 splice variants were measured in human RA synovium and RA patients' monocytes. In arthritic mice, the expression of the p41 CD74 isoform was significantly higher in severely affected paws compared with unaffected paws or the paws of naïve mice; the p41 isoform significantly correlated with the expression of TNF in arthritic paws. Compared with M2-like macrophages, M1-like macrophages expressed increased levels of CD74 and had higher expression, secretion and activity of CTSL. RA patients that responded to TNF blockade had significantly higher expression levels of CD74 in circulating monocytes after treatment, compared with non-responders. The expression of the human CD74 isoform a was significantly higher in RA synovia, compared with osteoarthritis synovia, and was associated with CSTL enzymatic activity. This study is the first to demonstrate differential expression of the CD74 p41 isoform in an auto-immune disorder and in response to therapy. The differential expression of CD74 splice variants indicates an association, and potentially a mechanistic role, in the pathogenesis of RA.
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Affiliation(s)
- Felix I L Clanchy
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Roosevelt Drive, Oxford, OX3 7FY, United Kingdom; Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK.
| | - Federica Borghese
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Roosevelt Drive, Oxford, OX3 7FY, United Kingdom
| | - Jonas Bystrom
- Centre for Translational Medicine & Therapeutics, William Harvey Research Institute, Queen Mary University of London, London, EC1M 6BQ, United Kingdom
| | - Attila Balog
- Department of Rheumatology and Immunology, Szent-Györgyi Albert Clinical Centre, University of Szeged, Szeged, Hungary
| | | | - Peter C Taylor
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Trevor W Stone
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Roosevelt Drive, Oxford, OX3 7FY, United Kingdom
| | - Rizgar A Mageed
- Centre for Translational Medicine & Therapeutics, William Harvey Research Institute, Queen Mary University of London, London, EC1M 6BQ, United Kingdom
| | - Richard O Williams
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Roosevelt Drive, Oxford, OX3 7FY, United Kingdom
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15
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Mitrović A, Senjor E, Jukić M, Bolčina L, Prunk M, Proj M, Nanut MP, Gobec S, Kos J. New inhibitors of cathepsin V impair tumor cell proliferation and elastin degradation and increase immune cell cytotoxicity. Comput Struct Biotechnol J 2022; 20:4667-4687. [PMID: 36147668 PMCID: PMC9459403 DOI: 10.1016/j.csbj.2022.08.046] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 08/19/2022] [Accepted: 08/20/2022] [Indexed: 11/26/2022] Open
Abstract
Identification of novel potent inhibitors of lysosomal cysteine peptidase cathepsin V. New inhibitors of cathepsin V demonstrated antitumor activity. They impair tumor cell proliferation and elastase degradation and increase immune cell cytotoxicity. Cathepsin V inhibitor impaired conversion of immunosuppressive factor cystatin F to its active monomeric form.
Cathepsin V is a human lysosomal cysteine peptidase with specific functions during pathological processes and is as such a promising therapeutic target. Peptidase inhibitors represent powerful pharmacological tools for regulating excessive proteolytic activity in various diseases. Cathepsin V is highly related to cathepsin L but differs in tissue distribution, binding site morphology, substrate specificity, and function. To validate its therapeutic potential and extend the number of potent and selective cathepsin V inhibitors, we used virtual high-throughput screening of commercially available compound libraries followed by an evaluation of kinetic properties to identify novel potent and selective cathepsin V inhibitors. We identified the ureido methylpiperidine carboxylate derivative, compound 7, as a reversible, selective, and potent inhibitor of cathepsin V. It also exhibited the most preferable characteristics for further evaluation with in vitro functional assays that simulate the processes in which cathepsin V is known to play an important role. Compound 7 exerted significant effects on cell proliferation, elastin degradation, and immune cell cytotoxicity. The latter was increased because compound 7 impaired conversion of immunosuppressive factor cystatin F to its active monomeric form. Taken together, our results present novel potent inhibitors of cathepsin V and provide new hit compounds for detailed development and optimization. Further, we demonstrate that cathepsin V is a potential target for new approaches to cancer therapy.
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Affiliation(s)
- Ana Mitrović
- Department of Biotechnology, Jožef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
- Corresponding author at: Department of Biotechnology, Jožef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia.
| | - Emanuela Senjor
- Department of Biotechnology, Jožef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Marko Jukić
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Lara Bolčina
- Department of Biotechnology, Jožef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Mateja Prunk
- Department of Biotechnology, Jožef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
| | - Matic Proj
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Milica Perišić Nanut
- Department of Biotechnology, Jožef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
| | - Stanislav Gobec
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Janko Kos
- Department of Biotechnology, Jožef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
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16
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Yoo Y, Choi E, Kim Y, Cha Y, Um E, Kim Y, Kim Y, Lee YS. Therapeutic potential of targeting cathepsin S in pulmonary fibrosis. Biomed Pharmacother 2021; 145:112245. [PMID: 34772578 DOI: 10.1016/j.biopha.2021.112245] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/18/2021] [Accepted: 09/22/2021] [Indexed: 11/16/2022] Open
Abstract
Cathepsin S (CTSS), a lysosomal protease, belongs to a family of cysteine cathepsin proteases that promote degradation of damaged proteins in the endolysosomal pathway. Aberrant CTSS expression and regulation are associated with the pathogenesis of several diseases, including lung diseases. CTSS overexpression causes a variety of pathological processes, including pulmonary fibrosis, with increased CTSS secretion and accelerated extracellular matrix remodeling. Compared to many other cysteine cathepsin family members, CTSS has unique features that it presents limited tissue expression and retains its enzymatic activity at a neutral pH, suggesting its decisive involvement in disease microenvironments. In this review, we investigated the role of CTSS in lung disease, exploring recent studies that have indicated that CTSS mediates fibrosis in unique ways, along with its structure, substrates, and distinct regulation. We also outlined examples of CTSS inhibitors in clinical and preclinical development and proposed CTSS as a potential therapeutic target for pulmonary fibrosis.
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Affiliation(s)
- YoungJo Yoo
- Graduate School of Pharmaceutical Sciences and College of Pharmacy, Ewha Womans University, Seoul 120-720, Republic of Korea
| | - Eun Choi
- Graduate School of Pharmaceutical Sciences and College of Pharmacy, Ewha Womans University, Seoul 120-720, Republic of Korea
| | - Yejin Kim
- Graduate School of Pharmaceutical Sciences and College of Pharmacy, Ewha Womans University, Seoul 120-720, Republic of Korea
| | - Yunyoung Cha
- Graduate School of Pharmaceutical Sciences and College of Pharmacy, Ewha Womans University, Seoul 120-720, Republic of Korea
| | - Eunhye Um
- Graduate School of Pharmaceutical Sciences and College of Pharmacy, Ewha Womans University, Seoul 120-720, Republic of Korea
| | - Younghwa Kim
- Graduate School of Pharmaceutical Sciences and College of Pharmacy, Ewha Womans University, Seoul 120-720, Republic of Korea
| | - Yunji Kim
- Graduate School of Pharmaceutical Sciences and College of Pharmacy, Ewha Womans University, Seoul 120-720, Republic of Korea
| | - Yun-Sil Lee
- Graduate School of Pharmaceutical Sciences and College of Pharmacy, Ewha Womans University, Seoul 120-720, Republic of Korea.
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17
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Tušar L, Usenik A, Turk B, Turk D. Mechanisms Applied by Protein Inhibitors to Inhibit Cysteine Proteases. Int J Mol Sci 2021; 22:ijms22030997. [PMID: 33498210 PMCID: PMC7863939 DOI: 10.3390/ijms22030997] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 01/13/2021] [Accepted: 01/16/2021] [Indexed: 02/07/2023] Open
Abstract
Protein inhibitors of proteases are an important tool of nature to regulate and control proteolysis in living organisms under physiological and pathological conditions. In this review, we analyzed the mechanisms of inhibition of cysteine proteases on the basis of structural information and compiled kinetic data. The gathered structural data indicate that the protein fold is not a major obstacle for the evolution of a protease inhibitor. It appears that nature can convert almost any starting fold into an inhibitor of a protease. In addition, there appears to be no general rule governing the inhibitory mechanism. The structural data make it clear that the “lock and key” mechanism is a historical concept with limited validity. However, the analysis suggests that the shape of the active site cleft of proteases imposes some restraints. When the S1 binding site is shaped as a pocket buried in the structure of protease, inhibitors can apply substrate-like binding mechanisms. In contrast, when the S1 binding site is in part exposed to solvent, the substrate-like inhibition cannot be employed. It appears that all proteases, with the exception of papain-like proteases, belong to the first group of proteases. Finally, we show a number of examples and provide hints on how to engineer protein inhibitors.
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Affiliation(s)
- Livija Tušar
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova cesta 39, 1000 Ljubljana, Slovenia; (L.T.); (A.U.); (B.T.)
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins (CIPKeBiP), Jamova cesta 39, 1000 Ljubljana, Slovenia
| | - Aleksandra Usenik
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova cesta 39, 1000 Ljubljana, Slovenia; (L.T.); (A.U.); (B.T.)
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins (CIPKeBiP), Jamova cesta 39, 1000 Ljubljana, Slovenia
| | - Boris Turk
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova cesta 39, 1000 Ljubljana, Slovenia; (L.T.); (A.U.); (B.T.)
- Faculty of Chemistry, University of Ljubljana, Večna pot 113, 1000 Ljubljana, Slovenia
- Institute of Regenerative Medicine, I.M. Sechenov First Moscow State Medical University, Bol’shaya Pirogovskaya Ulitsa, 19c1, 119146 Moscow, Russia
| | - Dušan Turk
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova cesta 39, 1000 Ljubljana, Slovenia; (L.T.); (A.U.); (B.T.)
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins (CIPKeBiP), Jamova cesta 39, 1000 Ljubljana, Slovenia
- Correspondence: ; Tel.: +386-1477-3857
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18
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Muñoz-Basagoiti J, Perez-Zsolt D, Carrillo J, Blanco J, Clotet B, Izquierdo-Useros N. SARS-CoV-2 Cellular Infection and Therapeutic Opportunities: Lessons Learned from Ebola Virus. MEMBRANES 2021; 11:64. [PMID: 33477477 PMCID: PMC7830673 DOI: 10.3390/membranes11010064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/24/2020] [Accepted: 01/04/2021] [Indexed: 11/29/2022]
Abstract
Viruses rely on the cellular machinery to replicate and propagate within newly infected individuals. Thus, viral entry into the host cell sets up the stage for productive infection and disease progression. Different viruses exploit distinct cellular receptors for viral entry; however, numerous viral internalization mechanisms are shared by very diverse viral families. Such is the case of Ebola virus (EBOV), which belongs to the filoviridae family, and the recently emerged coronavirus SARS-CoV-2. These two highly pathogenic viruses can exploit very similar endocytic routes to productively infect target cells. This convergence has sped up the experimental assessment of clinical therapies against SARS-CoV-2 previously found to be effective for EBOV, and facilitated their expedited clinical testing. Here we review how the viral entry processes and subsequent replication and egress strategies of EBOV and SARS-CoV-2 can overlap, and how our previous knowledge on antivirals, antibodies, and vaccines against EBOV has boosted the search for effective countermeasures against the new coronavirus. As preparedness is key to contain forthcoming pandemics, lessons learned over the years by combating life-threatening viruses should help us to quickly deploy effective tools against novel emerging viruses.
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Affiliation(s)
- Jordana Muñoz-Basagoiti
- IrsiCaixa AIDS Research Institute, Germans Trias I Pujol Research Institute (IGTP), Can Ruti Campus, 08916 Badalona, Spain; (J.M.-B.); (D.P.-Z.); (J.C.); (J.B.); (B.C.)
| | - Daniel Perez-Zsolt
- IrsiCaixa AIDS Research Institute, Germans Trias I Pujol Research Institute (IGTP), Can Ruti Campus, 08916 Badalona, Spain; (J.M.-B.); (D.P.-Z.); (J.C.); (J.B.); (B.C.)
| | - Jorge Carrillo
- IrsiCaixa AIDS Research Institute, Germans Trias I Pujol Research Institute (IGTP), Can Ruti Campus, 08916 Badalona, Spain; (J.M.-B.); (D.P.-Z.); (J.C.); (J.B.); (B.C.)
| | - Julià Blanco
- IrsiCaixa AIDS Research Institute, Germans Trias I Pujol Research Institute (IGTP), Can Ruti Campus, 08916 Badalona, Spain; (J.M.-B.); (D.P.-Z.); (J.C.); (J.B.); (B.C.)
- Infectious Diseases and Immunity Department, Faculty of Medicine, University of Vic (UVic-UCC), 08500 Vic, Spain
| | - Bonaventura Clotet
- IrsiCaixa AIDS Research Institute, Germans Trias I Pujol Research Institute (IGTP), Can Ruti Campus, 08916 Badalona, Spain; (J.M.-B.); (D.P.-Z.); (J.C.); (J.B.); (B.C.)
- Infectious Diseases and Immunity Department, Faculty of Medicine, University of Vic (UVic-UCC), 08500 Vic, Spain
- Infectious Diseases Department, Germans Trias i Pujol Hospital, 08916 Badalona, Spain
| | - Nuria Izquierdo-Useros
- IrsiCaixa AIDS Research Institute, Germans Trias I Pujol Research Institute (IGTP), Can Ruti Campus, 08916 Badalona, Spain; (J.M.-B.); (D.P.-Z.); (J.C.); (J.B.); (B.C.)
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19
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Dolenc I, Štefe I, Turk D, Taler-Verčič A, Turk B, Turk V, Stoka V. Human cathepsin X/Z is a biologically active homodimer. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1869:140567. [PMID: 33227497 DOI: 10.1016/j.bbapap.2020.140567] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 11/12/2020] [Accepted: 11/16/2020] [Indexed: 12/15/2022]
Abstract
Human cathepsin X belongs to the cathepsin family of 11 lysosomal cysteine proteases. We expressed recombinant procathepsin X in Pichia pastoris in vitro and cleaved it into its active mature form using aspartic cathepsin E. We found, using size exclusion chromatography, X-ray crystallography, and small-angle X-ray scattering, that cathepsin X is a biologically active homodimer with a molecular weight of ~53 kDa. The novel finding that cathepsin X is a dimeric protein opens new horizons in the understanding of its function and the underlying pathophysiological mechanisms of various diseases including neurodegenerative disorders in humans.
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Affiliation(s)
- Iztok Dolenc
- Department of Biochemistry and Molecular and Structural Biology, J. Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia.
| | - Ivica Štefe
- Department of Biochemistry and Molecular and Structural Biology, J. Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
| | - Dušan Turk
- Department of Biochemistry and Molecular and Structural Biology, J. Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia; Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova 39, SI-1000 Ljubljana, Slovenia
| | - Ajda Taler-Verčič
- Department of Biochemistry and Molecular and Structural Biology, J. Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
| | - Boris Turk
- Department of Biochemistry and Molecular and Structural Biology, J. Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
| | - Vito Turk
- Department of Biochemistry and Molecular and Structural Biology, J. Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia; Jožef Stefan International Postgraduate School, Jamova 39, SI-1000 Ljubljana, Slovenia.
| | - Veronika Stoka
- Department of Biochemistry and Molecular and Structural Biology, J. Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia.
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20
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Affiliation(s)
- Alexandra I Wells
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,Center for Microbial Pathogenesis, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Carolyn B Coyne
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA. .,Center for Microbial Pathogenesis, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
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21
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Bruchez A, Sha K, Johnson J, Chen L, Stefani C, McConnell H, Gaucherand L, Prins R, Matreyek KA, Hume AJ, Mühlberger E, Schmidt EV, Olinger GG, Stuart LM, Lacy-Hulbert A. MHC class II transactivator CIITA induces cell resistance to Ebola virus and SARS-like coronaviruses. Science 2020; 370:241-247. [PMID: 32855215 PMCID: PMC7665841 DOI: 10.1126/science.abb3753] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 08/20/2020] [Indexed: 01/01/2023]
Abstract
Recent outbreaks of Ebola virus (EBOV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have exposed our limited therapeutic options for such diseases and our poor understanding of the cellular mechanisms that block viral infections. Using a transposon-mediated gene-activation screen in human cells, we identify that the major histocompatibility complex (MHC) class II transactivator (CIITA) has antiviral activity against EBOV. CIITA induces resistance by activating expression of the p41 isoform of invariant chain CD74, which inhibits viral entry by blocking cathepsin-mediated processing of the Ebola glycoprotein. We further show that CD74 p41 can block the endosomal entry pathway of coronaviruses, including SARS-CoV-2. These data therefore implicate CIITA and CD74 in host defense against a range of viruses, and they identify an additional function of these proteins beyond their canonical roles in antigen presentation.
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MESH Headings
- Antigens, Differentiation, B-Lymphocyte/genetics
- Antigens, Differentiation, B-Lymphocyte/physiology
- Betacoronavirus/physiology
- COVID-19
- Cell Line, Tumor
- Coronavirus Infections/immunology
- Coronavirus Infections/virology
- DNA Transposable Elements
- Ebolavirus/physiology
- Endosomes/virology
- Genetic Testing
- Hemorrhagic Fever, Ebola/immunology
- Hemorrhagic Fever, Ebola/virology
- Histocompatibility Antigens Class II/genetics
- Histocompatibility Antigens Class II/physiology
- Host-Pathogen Interactions/genetics
- Host-Pathogen Interactions/immunology
- Humans
- Nuclear Proteins/genetics
- Nuclear Proteins/physiology
- Pandemics
- Pneumonia, Viral/immunology
- Pneumonia, Viral/virology
- SARS-CoV-2
- Trans-Activators/genetics
- Trans-Activators/physiology
- Transcription, Genetic
- Virus Internalization
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Affiliation(s)
- Anna Bruchez
- Benaroya Research Institute, Seattle, WA 98101, USA
| | - Ky Sha
- Benaroya Research Institute, Seattle, WA 98101, USA
| | - Joshua Johnson
- National Institute of Allergy and Infectious Diseases (NIAID) Integrated Research Facility, Frederick, MD 21702, USA
| | - Li Chen
- Massachusetts General Hospital, Boston, MA 02114, USA
| | | | | | | | - Rachel Prins
- Benaroya Research Institute, Seattle, WA 98101, USA
| | - Kenneth A Matreyek
- Department of Genome Sciences, University of Washington, Seattle, WA 98109, USA
| | - Adam J Hume
- Boston University School of Medicine, Boston, MA 02118, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02118, USA
| | - Elke Mühlberger
- Boston University School of Medicine, Boston, MA 02118, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02118, USA
| | | | - Gene G Olinger
- National Institute of Allergy and Infectious Diseases (NIAID) Integrated Research Facility, Frederick, MD 21702, USA
- Boston University School of Medicine, Boston, MA 02118, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02118, USA
- MRIGlobal, Gaithersburg, MD 20878, USA
| | - Lynda M Stuart
- Benaroya Research Institute, Seattle, WA 98101, USA
- Bill and Melinda Gates Foundation, Seattle, WA 98109, USA
| | - Adam Lacy-Hulbert
- Benaroya Research Institute, Seattle, WA 98101, USA.
- Department of Immunology, University of Washington, Seattle, WA 98109, USA
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22
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Poreba M, Groborz KM, Rut W, Pore M, Snipas SJ, Vizovisek M, Turk B, Kuhn P, Drag M, Salvesen GS. Multiplexed Probing of Proteolytic Enzymes Using Mass Cytometry-Compatible Activity-Based Probes. J Am Chem Soc 2020; 142:16704-16715. [PMID: 32870676 PMCID: PMC7595764 DOI: 10.1021/jacs.0c06762] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The subset of the proteome that contains enzymes in their catalytically active form can be interrogated by using probes targeted toward individual specific enzymes. A subset of such enzymes are proteases that are frequently studied with activity-based probes, small inhibitors equipped with a detectable tag, commonly a fluorophore. Due to the spectral overlap of these commonly used fluorophores, multiplex analysis becomes limited. To overcome this, we developed a series of protease-selective lanthanide-labeled probes compatible with mass cytometry giving us the ability to monitor the activity of multiple proteases in parallel. Using these probes, we were able to identify the distribution of four proteases with different active site geometries in three cell lines and peripheral blood mononuclear cells. This provides a framework for the use of mass cytometry for multiplexed enzyme activity detection.
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Affiliation(s)
- Marcin Poreba
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
- Wroclaw University of Science and Technology, Wroclaw, Poland
| | - Katarzyna M. Groborz
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
- Wroclaw University of Science and Technology, Wroclaw, Poland
| | - Wioletta Rut
- Wroclaw University of Science and Technology, Wroclaw, Poland
| | - Milind Pore
- University of Southern California, USC Michelson Center for Convergent Biosciences, Los Angeles, CA, USA
| | - Scott J. Snipas
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | | | - Boris Turk
- Jozef Stefan Institute, Ljubljana, Slovenia
| | - Peter Kuhn
- University of Southern California, USC Michelson Center for Convergent Biosciences, Los Angeles, CA, USA
| | - Marcin Drag
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
- Wroclaw University of Science and Technology, Wroclaw, Poland
| | - Guy S. Salvesen
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
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23
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Brown R, Nath S, Lora A, Samaha G, Elgamal Z, Kaiser R, Taggart C, Weldon S, Geraghty P. Cathepsin S: investigating an old player in lung disease pathogenesis, comorbidities, and potential therapeutics. Respir Res 2020; 21:111. [PMID: 32398133 PMCID: PMC7216426 DOI: 10.1186/s12931-020-01381-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 05/01/2020] [Indexed: 12/13/2022] Open
Abstract
Dysregulated expression and activity of cathepsin S (CTSS), a lysosomal protease and a member of the cysteine cathepsin protease family, is linked to the pathogenesis of multiple diseases, including a number of conditions affecting the lungs. Extracellular CTSS has potent elastase activity and by processing cytokines and host defense proteins, it also plays a role in the regulation of inflammation. CTSS has also been linked to G-coupled protein receptor activation and possesses an important intracellular role in major histocompatibility complex class II antigen presentation. Modulated CTSS activity is also associated with pulmonary disease comorbidities, such as cancer, cardiovascular disease, and diabetes. CTSS is expressed in a wide variety of immune cells and is biologically active at neutral pH. Herein, we review the significance of CTSS signaling in pulmonary diseases and associated comorbidities. We also discuss CTSS as a plausible therapeutic target and describe recent and current clinical trials examining CTSS inhibition as a means for treatment.
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Affiliation(s)
- Ryan Brown
- Airway Innate Immunity Research (AiiR) Group, Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Sridesh Nath
- Division of Pulmonary & Critical Care Medicine, Department of Medicine, State University of New York Downstate Medical Centre, Brooklyn, NY, USA
| | - Alnardo Lora
- Division of Pulmonary & Critical Care Medicine, Department of Medicine, State University of New York Downstate Medical Centre, Brooklyn, NY, USA
| | - Ghassan Samaha
- Division of Pulmonary & Critical Care Medicine, Department of Medicine, State University of New York Downstate Medical Centre, Brooklyn, NY, USA
| | - Ziyad Elgamal
- Division of Pulmonary & Critical Care Medicine, Department of Medicine, State University of New York Downstate Medical Centre, Brooklyn, NY, USA
| | - Ryan Kaiser
- Division of Pulmonary & Critical Care Medicine, Department of Medicine, State University of New York Downstate Medical Centre, Brooklyn, NY, USA
| | - Clifford Taggart
- Airway Innate Immunity Research (AiiR) Group, Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Sinéad Weldon
- Airway Innate Immunity Research (AiiR) Group, Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Patrick Geraghty
- Division of Pulmonary & Critical Care Medicine, Department of Medicine, State University of New York Downstate Medical Centre, Brooklyn, NY, USA.
- Department of Cell Biology, State University of New York Downstate Medical Centre, Brooklyn, NY, USA.
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24
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Jakoš T, Pišlar A, Jewett A, Kos J. Cysteine Cathepsins in Tumor-Associated Immune Cells. Front Immunol 2019; 10:2037. [PMID: 31555270 PMCID: PMC6724555 DOI: 10.3389/fimmu.2019.02037] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 08/12/2019] [Indexed: 12/23/2022] Open
Abstract
Cysteine cathepsins are key regulators of the innate and adaptive arms of the immune system. Their expression, activity, and subcellular localization are associated with the distinct development and differentiation stages of immune cells. They promote the activation of innate myeloid immune cells since they contribute to toll-like receptor signaling and to cytokine secretion. Furthermore, they control lysosomal biogenesis and autophagic flux, thus affecting innate immune cell survival and polarization. They also regulate bidirectional communication between the cell exterior and the cytoskeleton, thus influencing cell interactions, morphology, and motility. Importantly, cysteine cathepsins contribute to the priming of adaptive immune cells by controlling antigen presentation and are involved in cytotoxic granule mediated killing in cytotoxic T lymphocytes and natural killer cells. Cathepins'aberrant activity can be prevented by their endogenous inhibitors, cystatins. However, dysregulated proteolysis contributes significantly to tumor progression also by modulation of the antitumor immune response. Especially tumor-associated myeloid cells, such as tumor-associated macrophages and myeloid-derived suppressor cells, which are known for their tumor promoting and immunosuppressive functions, constitute the major source of excessive cysteine cathepsin activity in cancer. Since they are enriched in the tumor microenvironment, cysteine cathepsins represent exciting targets for development of new diagnostic and therapeutic moieties.
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Affiliation(s)
- Tanja Jakoš
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Anja Pišlar
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Anahid Jewett
- UCLA School of Dentistry and Medicine, Los Angeles, CA, United States
| | - Janko Kos
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia.,Department of Biotechnology, Jožef Stefan Institute, Ljubljana, Slovenia
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25
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Poreba M, Groborz K, Vizovisek M, Maruggi M, Turk D, Turk B, Powis G, Drag M, Salvesen GS. Fluorescent probes towards selective cathepsin B detection and visualization in cancer cells and patient samples. Chem Sci 2019; 10:8461-8477. [PMID: 31803426 PMCID: PMC6839509 DOI: 10.1039/c9sc00997c] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 07/29/2019] [Indexed: 12/23/2022] Open
Abstract
Highly selective fluorescent activity-based probe for the visualization of cathepsin B in cancer cells.
Human cysteine cathepsins constitute an 11-membered family of proteases responsible for degradation of proteins in cellular endosomal–lysosomal compartments as such, they play important roles in antigen processing, cellular stress signaling, autophagy, and senescence. Moreover, for many years these enzymes were also linked to tumor growth, invasion, angiogenesis and metastasis when upregulated. Individual biological roles of each cathepsin are difficult to establish, because of their redundancy and similar substrate specificities. Selective chemical tools that enable imaging of individual cathepsin activities in living cells, tumors, and the tumor microenvironment may provide a better insight into their functions. In this work, we used HyCoSuL technology to profile the substrate specificity of human cathepsin B. The use of unnatural amino acids in the substrate library enabled us to uncover the broad cathepsin B preferences that we utilized to design highly-selective substrates and fluorescent activity-based probes (ABPs). We further demonstrated that Cy5-labeled MP-CB-2 probe can selectively label cathepsin B in eighteen cancer cell lines tested, making this ABP highly suitable for other biological setups. Moreover, using Cy5-labelled MP-CB-2 we were able to demonstrate by fluorescence microscopy that in cancer cells cathepsins B and L share overlapping, but not identical subcellular localization.
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Affiliation(s)
- Marcin Poreba
- Sanford Burnham Prebys Medical Discovery Institute , 10901 North Torrey Pines Road , La Jolla , CA 92037 , USA . ; ; .,Department of Bioorganic Chemistry , Faculty of Chemistry , Wroclaw University of Technology , Wyb. Wyspianskiego 27 , 50-370 Wroclaw , Poland
| | - Katarzyna Groborz
- Department of Bioorganic Chemistry , Faculty of Chemistry , Wroclaw University of Technology , Wyb. Wyspianskiego 27 , 50-370 Wroclaw , Poland
| | - Matej Vizovisek
- Department of Biochemistry and Molecular and Structural Biology , Jožef Stefan Institute , SI-1000 Ljubljana , Slovenia
| | - Marco Maruggi
- Sanford Burnham Prebys Medical Discovery Institute , 10901 North Torrey Pines Road , La Jolla , CA 92037 , USA . ; ;
| | - Dusan Turk
- Department of Biochemistry and Molecular and Structural Biology , Jožef Stefan Institute , SI-1000 Ljubljana , Slovenia
| | - Boris Turk
- Department of Biochemistry and Molecular and Structural Biology , Jožef Stefan Institute , SI-1000 Ljubljana , Slovenia.,Faculty of Chemistry and Chemical Technology , University of Ljubljana , SI-1000 Ljubljana , Slovenia
| | - Garth Powis
- Sanford Burnham Prebys Medical Discovery Institute , 10901 North Torrey Pines Road , La Jolla , CA 92037 , USA . ; ;
| | - Marcin Drag
- Sanford Burnham Prebys Medical Discovery Institute , 10901 North Torrey Pines Road , La Jolla , CA 92037 , USA . ; ; .,Department of Bioorganic Chemistry , Faculty of Chemistry , Wroclaw University of Technology , Wyb. Wyspianskiego 27 , 50-370 Wroclaw , Poland
| | - Guy S Salvesen
- Sanford Burnham Prebys Medical Discovery Institute , 10901 North Torrey Pines Road , La Jolla , CA 92037 , USA . ; ;
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26
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Bratovš A, Kramer L, Mikhaylov G, Vasiljeva O, Turk B. Stefin A-functionalized liposomes as a system for cathepsins S and L-targeted drug delivery. Biochimie 2019; 166:94-102. [PMID: 31163196 DOI: 10.1016/j.biochi.2019.05.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Accepted: 05/30/2019] [Indexed: 01/26/2023]
Abstract
Proteolytic activity in the tumor microenvironment is one of the key elements supporting tumor development and metastasis. One of the key families of proteases that are overexpressed in various types of cancer and implicated in different stages of tumor progression are cysteine cathepsins. Among them, cathepsins S and L can be secreted into the tumor microenvironment by tumor and/or immune cells, making them promising drug delivery targets. Here we present a new system for cathepsin S/L targeting using a liposomal drug carrier system functionalized with the endogenous cysteine cathepsin inhibitor, stefin A. The selective targeting of cathepsins by stefin A-conjugated liposomes was confirmed in vitro and in vivo, demonstrating the potential of this approach for cancer diagnosis and treatment.
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Affiliation(s)
- Andreja Bratovš
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia; Jozef Stefan International Postgraduate School, Jamova 39, Sl-1000 Ljubljana, Slovenia
| | - Lovro Kramer
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
| | - Georgy Mikhaylov
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
| | - Olga Vasiljeva
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia.
| | - Boris Turk
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia; Faculty of Chemistry and Chemical Technology, Večna Pot 113, University of Ljubljana, SI-1000 Ljubljana, Slovenia.
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Semple SL, Heath G, Christie D, Braunstein M, Kales SC, Dixon B. Immune stimulation of rainbow trout reveals divergent regulation of MH class II-associated invariant chain isoforms. Immunogenetics 2019; 71:407-420. [PMID: 31037384 DOI: 10.1007/s00251-019-01115-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Accepted: 04/06/2019] [Indexed: 12/20/2022]
Abstract
Major histocompatibility complex (MHC) class II-associated invariant chain is a chaperone responsible for targeting the MHC class II dimer to the endocytic pathway, thus enabling the loading of exogenous antigens onto the MHC class II receptor. In the current study, in vivo and in vitro methods were used to investigate the regulation of the rainbow trout invariant chain proteins S25-7 and INVX, upon immune system activation. Whole rainbow trout and the macrophage/monocyte-like cell line RTS11 were treated with PMA at concentrations shown to induce IL-1β transcripts and homotypic aggregation of RTS11. S25-7 transcript levels remained unchanged in the gill, spleen, and liver and were found to be significantly decreased in head kidney beginning 24 h post-stimulation. Meanwhile, INVX transcript levels remained unchanged in all tissues studied. Both S25-7 and INVX proteins were produced in gill and spleen tissues but their expression was unaffected by immune system stimulation. Surprisingly, neither INVX nor S25-7 protein was detected in the secondary immune organ, the head kidney. Analysis of RTS11 cultures demonstrated that both INVX and S25-7 transcript levels significantly increased at 96 h and 120 h following PMA stimulation before returning to control levels at 168 h. Meanwhile, at the protein level in RTS11, S25-7 remained unchanged while INVX had a significant decrease at 168 h post-stimulation. These results indicate that neither INVX nor S25-7 is upregulated upon immune system activation; thus, teleosts have evolved a system of immune regulation that is different than that found in mammals.
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Affiliation(s)
- Shawna L Semple
- Department of Biology, University of Waterloo, 200 University Ave W., Waterloo, ON, N2L 3G1, Canada
| | - George Heath
- Department of Biology, University of Waterloo, 200 University Ave W., Waterloo, ON, N2L 3G1, Canada
| | - Darah Christie
- Department of Biology, University of Waterloo, 200 University Ave W., Waterloo, ON, N2L 3G1, Canada
| | - Marsela Braunstein
- Department of Biology, University of Waterloo, 200 University Ave W., Waterloo, ON, N2L 3G1, Canada
| | - Stephen C Kales
- Department of Biology, University of Waterloo, 200 University Ave W., Waterloo, ON, N2L 3G1, Canada
| | - Brian Dixon
- Department of Biology, University of Waterloo, 200 University Ave W., Waterloo, ON, N2L 3G1, Canada.
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Thibodeau J, Moulefera MA, Balthazard R. On the structure–function of MHC class II molecules and how single amino acid polymorphisms could alter intracellular trafficking. Hum Immunol 2019; 80:15-31. [DOI: 10.1016/j.humimm.2018.10.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 09/25/2018] [Accepted: 10/01/2018] [Indexed: 12/01/2022]
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Ancient features of the MHC class II presentation pathway, and a model for the possible origin of MHC molecules. Immunogenetics 2018; 71:233-249. [DOI: 10.1007/s00251-018-1090-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 10/06/2018] [Indexed: 10/28/2022]
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30
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Poreba M, Rut W, Vizovisek M, Groborz K, Kasperkiewicz P, Finlay D, Vuori K, Turk D, Turk B, Salvesen GS, Drag M. Selective imaging of cathepsin L in breast cancer by fluorescent activity-based probes. Chem Sci 2018; 9:2113-2129. [PMID: 29719685 PMCID: PMC5896380 DOI: 10.1039/c7sc04303a] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 01/15/2018] [Indexed: 11/21/2022] Open
Abstract
Highly-selective fluorogenic substrate and activity-based probe for monitoring cathepsin L activity in the breast cancer cell line MDA-MB-231.
Cysteine cathepsins normally function in the lysosomal degradation system where they are critical for the maintenance of cellular homeostasis and the MHC II immune response, and have been found to have major roles in several diseases and in tumor progression. Selective visualization of individual protease activity within a complex proteome is of major importance to establish their roles in both normal and tumor cells, thereby facilitating our understanding of the regulation of proteolytic networks. A generally accepted means to monitor protease activity is the use of small molecule substrates and activity-based probes. However, there are eleven human cysteine cathepsins, with a few of them displaying overlapping substrate specificity, making the development of small molecules that selectively target a single cathepsin very challenging. Here, we utilized HyCoSuL, a positional scanning substrate approach, to develop a highly-selective fluorogenic substrate and activity-based probe for monitoring cathepsin L activity in the breast cancer cell line MDA-MB-231. Use of this probe enabled us to distinguish the activity of cathepsin L from that of other cathepsins, particularly cathepsin B, which is abundant and ubiquitously expressed in normal and transformed cell types. We found that cathepsin L localization in MDA-MB-231 cells greatly overlaps with that of cathepsin B, however, several cathepsin L-rich lysosomes lacked cathepsin B activity. Overall, these studies demonstrate that HyCoSuL-derived small molecule probes are valuable tools to image cathepsin L activity in living cells. This approach thus enables evaluation of cathepsin L function in tumorigenesis and is applicable to other cysteine cathepsins.
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Affiliation(s)
- Marcin Poreba
- Department of Bioorganic Chemistry , Faculty of Chemistry , Wroclaw University of Technology , Wyb. Wyspianskiego 27 , 50-370 Wroclaw , Poland . ; .,Sanford Burnham Prebys Medical Discovery Institute , 10901 North Torrey Pines Road , La Jolla , CA 92037 , USA
| | - Wioletta Rut
- Department of Bioorganic Chemistry , Faculty of Chemistry , Wroclaw University of Technology , Wyb. Wyspianskiego 27 , 50-370 Wroclaw , Poland . ;
| | - Matej Vizovisek
- Department of Biochemistry and Molecular and Structural Biology , Jožef Stefan Institute , SI-1000 Ljubljana , Slovenia
| | - Katarzyna Groborz
- Department of Bioorganic Chemistry , Faculty of Chemistry , Wroclaw University of Technology , Wyb. Wyspianskiego 27 , 50-370 Wroclaw , Poland . ;
| | - Paulina Kasperkiewicz
- Department of Bioorganic Chemistry , Faculty of Chemistry , Wroclaw University of Technology , Wyb. Wyspianskiego 27 , 50-370 Wroclaw , Poland . ; .,Sanford Burnham Prebys Medical Discovery Institute , 10901 North Torrey Pines Road , La Jolla , CA 92037 , USA
| | - Darren Finlay
- Sanford Burnham Prebys Medical Discovery Institute , 10901 North Torrey Pines Road , La Jolla , CA 92037 , USA
| | - Kristiina Vuori
- Sanford Burnham Prebys Medical Discovery Institute , 10901 North Torrey Pines Road , La Jolla , CA 92037 , USA
| | - Dusan Turk
- Department of Biochemistry and Molecular and Structural Biology , Jožef Stefan Institute , SI-1000 Ljubljana , Slovenia
| | - Boris Turk
- Department of Biochemistry and Molecular and Structural Biology , Jožef Stefan Institute , SI-1000 Ljubljana , Slovenia
| | - Guy S Salvesen
- Sanford Burnham Prebys Medical Discovery Institute , 10901 North Torrey Pines Road , La Jolla , CA 92037 , USA
| | - Marcin Drag
- Department of Bioorganic Chemistry , Faculty of Chemistry , Wroclaw University of Technology , Wyb. Wyspianskiego 27 , 50-370 Wroclaw , Poland . ;
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Vidmar R, Vizovišek M, Turk D, Turk B, Fonović M. Protease cleavage site fingerprinting by label-free in-gel degradomics reveals pH-dependent specificity switch of legumain. EMBO J 2017; 36:2455-2465. [PMID: 28733325 DOI: 10.15252/embj.201796750] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 06/29/2017] [Accepted: 07/03/2017] [Indexed: 01/09/2023] Open
Abstract
Determination of protease specificity is of crucial importance for understanding protease function. We have developed the first gel-based label-free proteomic approach (DIPPS-direct in-gel profiling of protease specificity) that enables quick and reliable determination of protease cleavage specificities under large variety of experimental conditions. The methodology is based on in-gel digestion of the gel-separated proteome with the studied protease, enrichment of cleaved peptides by gel extraction, and subsequent mass spectrometry analysis combined with a length-limited unspecific database search. We applied the methodology to profile ten proteases ranging from highly specific (trypsin, endoproteinase GluC, caspase-7, and legumain) to broadly specific (matrix-metalloproteinase-3, thermolysin, and cathepsins K, L, S, and V). Using DIPPS, we were able to perform specificity profiling of thermolysin at its optimal temperature of 75°C, which confirmed the applicability of the method to extreme experimental conditions. Moreover, DIPPS enabled the first global specificity profiling of legumain at pH as low as 4.0, which revealed a pH-dependent change in the specificity of this protease, further supporting its broad applicability.
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Affiliation(s)
- Robert Vidmar
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Ljubljana, Slovenia.,International Postgraduate School Jožef Stefan, Ljubljana, Slovenia
| | - Matej Vizovišek
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Dušan Turk
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Ljubljana, Slovenia.,International Postgraduate School Jožef Stefan, Ljubljana, Slovenia.,Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Ljubljana, Slovenia
| | - Boris Turk
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Ljubljana, Slovenia .,Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Ljubljana, Slovenia.,Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | - Marko Fonović
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Ljubljana, Slovenia .,Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Ljubljana, Slovenia
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Zavašnik-Bergant T, Vidmar R, Sekirnik A, Fonović M, Salát J, Grunclová L, Kopáček P, Turk B. Salivary Tick Cystatin OmC2 Targets Lysosomal Cathepsins S and C in Human Dendritic Cells. Front Cell Infect Microbiol 2017; 7:288. [PMID: 28713775 PMCID: PMC5492865 DOI: 10.3389/fcimb.2017.00288] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 06/14/2017] [Indexed: 11/14/2022] Open
Abstract
To ensure successful feeding tick saliva contains a number of inhibitory proteins that interfere with the host immune response and help to create a permissive environment for pathogen transmission. Among the potential targets of the salivary cystatins are two host cysteine proteases, cathepsin S, which is essential for antigen- and invariant chain-processing, and cathepsin C (dipeptidyl peptidase 1, DPP1), which plays a critical role in processing and activation of the granule serine proteases. Here, the effect of salivary cystatin OmC2 from Ornithodoros moubata was studied using differentiated MUTZ-3 cells as a model of immature dendritic cells of the host skin. Following internalization, cystatin OmC2 was initially found to inhibit the activity of several cysteine cathepsins, as indicated by the decreased rates of degradation of fluorogenic peptide substrates. To identify targets, affinity chromatography was used to isolate His-tagged cystatin OmC2 together with the bound proteins from MUTZ-3 cells. Cathepsins S and C were identified in these complexes by mass spectrometry and confirmed by immunoblotting. Furthermore, reduced increase in the surface expression of MHC II and CD86, which are associated with the maturation of dendritic cells, was observed. In contrast, human inhibitor cystatin C, which is normally expressed and secreted by dendritic cells, did not affect the expression of CD86. It is proposed that internalization of salivary cystatin OmC2 by the host dendritic cells targets cathepsins S and C, thereby affecting their maturation.
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Affiliation(s)
- Tina Zavašnik-Bergant
- Department of Biochemistry, Molecular and Structural Biology, Jožef Stefan InstituteLjubljana, Slovenia
| | - Robert Vidmar
- Department of Biochemistry, Molecular and Structural Biology, Jožef Stefan InstituteLjubljana, Slovenia
| | - Andreja Sekirnik
- Department of Biochemistry, Molecular and Structural Biology, Jožef Stefan InstituteLjubljana, Slovenia
| | - Marko Fonović
- Department of Biochemistry, Molecular and Structural Biology, Jožef Stefan InstituteLjubljana, Slovenia
| | - Jiří Salát
- Institute of Parasitology, Biology Centre of the Czech Academy of SciencesČeské Budějovice, Czechia
| | - Lenka Grunclová
- Institute of Parasitology, Biology Centre of the Czech Academy of SciencesČeské Budějovice, Czechia
| | - Petr Kopáček
- Institute of Parasitology, Biology Centre of the Czech Academy of SciencesČeské Budějovice, Czechia
| | - Boris Turk
- Department of Biochemistry, Molecular and Structural Biology, Jožef Stefan InstituteLjubljana, Slovenia.,Centre of Excellence for Integrated Approaches in Chemistry and Biology of ProteinsLjubljana, Slovenia.,Faculty of Chemistry and Chemical Technology, University of LjubljanaLjubljana, Slovenia
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Cystatin C deficiency suppresses tumor growth in a breast cancer model through decreased proliferation of tumor cells. Oncotarget 2017; 8:73793-73809. [PMID: 29088746 PMCID: PMC5650301 DOI: 10.18632/oncotarget.17379] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 03/22/2017] [Indexed: 01/01/2023] Open
Abstract
Cysteine cathepsins are proteases that, in addition to their important physiological functions, have been associated with multiple pathologies, including cancer. Cystatin C (CstC) is a major endogenous inhibitor that regulates the extracellular activity of cysteine cathepsins. We investigated the role of cystatin C in mammary cancer using CstC knockout mice and a mouse model of breast cancer induced by expression of the polyoma middle T oncoprotein (PyMT) in the mammary epithelium. We showed that the ablation of CstC reduced the rate of mammary tumor growth. Notably, a decrease in the proliferation of CstC knockout PyMT tumor cells was demonstrated ex vivo and in vitro, indicating a role for this protease inhibitor in signaling pathways that control cell proliferation. An increase in phosphorylated p-38 was observed in CstC knockout tumors, suggesting a novel function for cystatin C in cancer development, independent of the TGF-β pathway. Moreover, proteomic analysis of the CstC wild-type and knockout PyMT primary cell secretomes revealed a decrease in the levels of 14-3-3 proteins in the secretome of knock-out cells, suggesting a novel link between cysteine cathepsins, cystatin C and 14-3-3 proteins in tumorigenesis, calling for further investigations.
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34
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Invariant Chain Complexes and Clusters as Platforms for MIF Signaling. Cells 2017; 6:cells6010006. [PMID: 28208600 PMCID: PMC5371871 DOI: 10.3390/cells6010006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 02/05/2017] [Accepted: 02/07/2017] [Indexed: 12/24/2022] Open
Abstract
Invariant chain (Ii/CD74) has been identified as a surface receptor for migration inhibitory factor (MIF). Most cells that express Ii also synthesize major histocompatibility complex class II (MHC II) molecules, which depend on Ii as a chaperone and a targeting factor. The assembly of nonameric complexes consisting of one Ii trimer and three MHC II molecules (each of which is a heterodimer) has been regarded as a prerequisite for efficient delivery to the cell surface. Due to rapid endocytosis, however, only low levels of Ii-MHC II complexes are displayed on the cell surface of professional antigen presenting cells and very little free Ii trimers. The association of Ii and MHC II has been reported to block the interaction with MIF, thus questioning the role of surface Ii as a receptor for MIF on MHC II-expressing cells. Recent work offers a potential solution to this conundrum: Many Ii-complexes at the cell surface appear to be under-saturated with MHC II, leaving unoccupied Ii subunits as potential binding sites for MIF. Some of this work also sheds light on novel aspects of signal transduction by Ii-bound MIF in B-lymphocytes: membrane raft association of Ii-MHC II complexes enables MIF to target Ii-MHC II to antigen-clustered B-cell-receptors (BCR) and to foster BCR-driven signaling and intracellular trafficking.
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Rangel CK, Parizi LF, Sabadin GA, Costa EP, Romeiro NC, Isezaki M, Githaka NW, Seixas A, Logullo C, Konnai S, Ohashi K, da Silva Vaz I. Molecular and structural characterization of novel cystatins from the taiga tick Ixodes persulcatus. Ticks Tick Borne Dis 2017; 8:432-441. [PMID: 28174118 DOI: 10.1016/j.ttbdis.2017.01.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 01/27/2017] [Accepted: 01/27/2017] [Indexed: 11/19/2022]
Abstract
Cystatins are cysteine peptidase inhibitors that in ticks mediate processes such as blood feeding and digestion. The ixodid tick Ixodes persulcatus is endemic to the Eurasia, where it is the principal vector of Lyme borreliosis. To date, no I. persulcatus cystatin has been characterized. In the present work, we describe three novel cystatins from I. persulcatus, named JpIpcys2a, JpIpcys2b and JpIpcys2c. In addition, the potential of tick cystatins as cross-protective antigens was evaluated by vaccination of hamsters using BrBmcys2c, a cystatin from Rhipicephalus microplus, against I. persulcatus infestation. Sequence analysis showed that motifs that are characteristic of cystatins type 2 are fully conserved in JpIpcys2b, while mutations are present in both JpIpcys2a and JpIpcys2c. Protein-protein docking simulations further revealed that JpIpcys2a, JpIpcys2b and JpIpcys2c showed conserved binding sites to human cathepsins L, all of them covering the active site cleft. Cystatin transcripts were detected in different I. persulcatus tissues and instars, showing their ubiquitous expression during I. persulcatus development. Serological analysis showed that although hamsters immunized with BrBmcys2c developed a humoral immune response, this response was not adequate to protect against a heterologous challenge with I. persulcatus adult ticks. The lack of cross-protection provided by BrBmcys2c immunization is perhaps linked to the fact that cystatins cluster into multigene protein families that are expressed differentially and exhibit functional redundancy. How to target such small proteins that are secreted in low quantities remains a challenge in the development of suitable anti-tick vaccine antigens.
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Affiliation(s)
- Carolina K Rangel
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves, 9500, Prédio 43421, Porto Alegre 91501-970, RS, Brazil
| | - Luís F Parizi
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves, 9500, Prédio 43421, Porto Alegre 91501-970, RS, Brazil; Laboratory of Infectious Diseases, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, 060-0818, Sapporo, Hokkaido, Japan
| | - Gabriela A Sabadin
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves, 9500, Prédio 43421, Porto Alegre 91501-970, RS, Brazil
| | - Evenilton P Costa
- Unidade de Experimentação Animal, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Avenida Alberto Lamego, 2000, Campos dos Goytacases, 28035-200, RJ, Brazil
| | - Nelilma C Romeiro
- LICC-Laboratório Integrado de Computação Científica-Universidade Federal do Rio de Janeiro-Campus Macaé, Macaé, 27901-000, RJ, Brazil
| | - Masayoshi Isezaki
- Laboratory of Infectious Diseases, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, 060-0818, Sapporo, Hokkaido, Japan
| | - Naftaly W Githaka
- Laboratory of Infectious Diseases, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, 060-0818, Sapporo, Hokkaido, Japan
| | - Adriana Seixas
- Departamento de Farmacociências, Universidade Federal de Ciências da Saúde de Porto Alegre, Rua Sarmento Leite, 245, Porto Alegre 90050-170, RS, Brazil; Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular, Brazil
| | - Carlos Logullo
- Unidade de Experimentação Animal, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Avenida Alberto Lamego, 2000, Campos dos Goytacases, 28035-200, RJ, Brazil; Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular, Brazil
| | - Satoru Konnai
- Laboratory of Infectious Diseases, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, 060-0818, Sapporo, Hokkaido, Japan
| | - Kazuhiko Ohashi
- Laboratory of Infectious Diseases, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, 060-0818, Sapporo, Hokkaido, Japan
| | - Itabajara da Silva Vaz
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves, 9500, Prédio 43421, Porto Alegre 91501-970, RS, Brazil; Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves, 9090, Porto Alegre 91540-000, RS, Brazil; Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular, Brazil.
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Ben-Nun Y, Fichman G, Adler-Abramovich L, Turk B, Gazit E, Blum G. Cathepsin nanofiber substrates as potential agents for targeted drug delivery. J Control Release 2016; 257:60-67. [PMID: 27908759 DOI: 10.1016/j.jconrel.2016.11.028] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 11/19/2016] [Accepted: 11/24/2016] [Indexed: 10/20/2022]
Abstract
The development of reactive drug carriers that could actively respond to biological signals is a challenging task. Different peptides can self-assemble into biocompatible nanostructures of various functionalities, including drugs carriers. Minimal building blocks, such as diphenylalanine, readily form ordered nanostructures. Here we present the development of self-assembled tetra-peptides that include the diphenylalanine motif, serving as substrates of the cathepsin proteases. This is of great clinical importance as cathepsins, whose activity and expression are highly elevated in cancer and other pathologies, have been shown to serve as efficient enzymes for therapeutic release. Based on the cathepsins affinity around the active site, we generated a library of Phe-Phe-Lys-Phe (FFKF) tetra-peptide substrates (TPSs). We inserted various N-termini capping groups with different chemical properties to investigate the effect on protease affinity and self-assembly. All nine TPSs were cleaved by their targets, cathepsins B and L. However, solvent switching led to nanofibers self-assembly of only seven of them. Due to its rapid self-assembly and complete degradation by cathepsin B, we focused on TPS4, Cbz-FFKF-OH. Degradation of TPS4 nanofibers by cathepsin B led to the release of 91.8±0.3% of the incorporated anti-cancerous drug Doxorubicin from the nanofibers within 8h while only 55±0.2% was released without enzyme treatment. Finally, we demonstrated that tumor lysates fully degraded TPS4 nanofibers. Collectively, these results suggest that tetra-peptide substrates that form nanostructures could serve as a promising platform for targeted drug delivery to pathologies in which protease activity is highly elevated.
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Affiliation(s)
- Yael Ben-Nun
- The Institute for Drug Research, School of Pharmacy, Faculty of Medicine, Hebrew University, Jerusalem, Israel
| | - Galit Fichman
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Lihi Adler-Abramovich
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Boris Turk
- Department of Biochemistry and Molecular Biology, J. Stefan Institute, Ljubljana, Slovenia; Faculty of Chemistry and Chemical Technology, University of Ljubljana, Slovenia; Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova cesta 39, SI-1000 Ljubljana, Slovenia
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel; Department of Materials Science and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv, Israel
| | - Galia Blum
- The Institute for Drug Research, School of Pharmacy, Faculty of Medicine, Hebrew University, Jerusalem, Israel.
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Öhrvik H, Logeman B, Turk B, Reinheckel T, Thiele DJ. Cathepsin Protease Controls Copper and Cisplatin Accumulation via Cleavage of the Ctr1 Metal-binding Ectodomain. J Biol Chem 2016; 291:13905-13916. [PMID: 27143361 DOI: 10.1074/jbc.m116.731281] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Indexed: 11/06/2022] Open
Abstract
Copper is an essential metal ion for embryonic development, iron acquisition, cardiac function, neuropeptide biogenesis, and other critical physiological processes. Ctr1 is a high affinity Cu(+) transporter on the plasma membrane and endosomes that exists as a full-length protein and a truncated form of Ctr1 lacking the methionine- and histidine-rich metal-binding ectodomain, and it exhibits reduced Cu(+) transport activity. Here, we identify the cathepsin L/B endolysosomal proteases functioning in a direct and rate-limiting step in the Ctr1 ectodomain cleavage. Cells and mice lacking cathepsin L accumulate full-length Ctr1 and hyper-accumulate copper. As Ctr1 also transports the chemotherapeutic drug cisplatin via direct binding to the ectodomain, we demonstrate that the combination of cisplatin with a cathepsin L/B inhibitor enhances cisplatin uptake and cell killing. These studies identify a new processing event and the key protease that cleaves the Ctr1 metal-binding ectodomain, which functions to regulate cellular Cu(+) and cisplatin acquisition.
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Affiliation(s)
- Helena Öhrvik
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina 27710.
| | - Brandon Logeman
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina 27710
| | - Boris Turk
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, SI-1000 Ljubljana, Slovenia; Faculty of Chemistry and Chemical Technology, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Thomas Reinheckel
- Institute of Molecular Medicine and Cell Research, Medical Faculty, Freiburg 79104 Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg 79104 Germany
| | - Dennis J Thiele
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina 27710; Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710; Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina 27710.
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38
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Sosnowski P, Turk D. Caught in the act: the crystal structure of cleaved cathepsin L bound to the active site of Cathepsin L. FEBS Lett 2016; 590:1253-61. [PMID: 26992470 DOI: 10.1002/1873-3468.12140] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 03/10/2016] [Accepted: 03/15/2016] [Indexed: 12/13/2022]
Abstract
Cathepsin L is a ubiquitously expressed papain-like cysteine protease involved in the endosomal degradation of proteins and has numerous roles in physiological and pathological processes, such as arthritis, osteoporosis, and cancer. Insight into the specificity of cathepsin L is important for elucidating its physiological roles and drug discovery. To study interactions with synthetic ligands, we prepared a presumably inactive mutant and crystallized it. Unexpectedly, the crystal structure determined at 1.4 Å revealed that the cathepsin L molecule is cleaved, with the cleaved region trapped in the active site cleft of the neighboring molecule. Hence, the catalytic mutant demonstrated low levels of catalytic activity.
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Affiliation(s)
- Piotr Sosnowski
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Slovenia.,International Postgraduate School Jozef Stefan, Ljubljana, Slovenia
| | - Dušan Turk
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Slovenia.,International Postgraduate School Jozef Stefan, Ljubljana, Slovenia.,Jozef Stefan Institute, Ljubljana, Slovenia
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39
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Schröder B. The multifaceted roles of the invariant chain CD74--More than just a chaperone. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1863:1269-81. [PMID: 27033518 DOI: 10.1016/j.bbamcr.2016.03.026] [Citation(s) in RCA: 140] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 03/22/2016] [Accepted: 03/23/2016] [Indexed: 01/13/2023]
Abstract
The invariant chain (CD74) is well known for its essential role in antigen presentation by mediating assembly and subcellular trafficking of the MHCII complex. Beyond this, CD74 has also been implicated in a number of processes independent of MHCII. These include the regulation of endosomal trafficking, cell migration and cellular signalling as surface receptor of the pro-inflammatory cytokine macrophage migration inhibitory factor (MIF). In several forms of cancer, CD74 is up-regulated and associated with enhanced proliferation and metastatic potential. In this review, an overview of the diverse biological functions of the CD74 protein is provided with a particular focus on how these may be regulated. In particular, proteolysis of CD74 will be discussed as a central mechanism to control the actions of this important protein at different levels.
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Affiliation(s)
- Bernd Schröder
- Biochemical Institute, Christian Albrechts University of Kiel, Otto-Hahn-Platz 9, D-24118 Kiel, Germany.
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40
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Zavašnik-Bergant T, Bergant Marušič M. Exogenous Thyropin from p41 Invariant Chain Diminishes Cysteine Protease Activity and Affects IL-12 Secretion during Maturation of Human Dendritic Cells. PLoS One 2016; 11:e0150815. [PMID: 26960148 PMCID: PMC4784741 DOI: 10.1371/journal.pone.0150815] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 02/19/2016] [Indexed: 12/31/2022] Open
Abstract
Dendritic cells (DC) play a pivotal role as antigen presenting cells (APC) and their maturation is crucial for effectively eliciting an antigen-specific immune response. The p41 splice variant of MHC class II-associated chaperone, called invariant chain p41 Ii, contains an amino acid sequence, the p41 fragment, which is a thyropin-type inhibitor of proteolytic enzymes. The effects of exogenous p41 fragment and related thyropin inhibitors acting on human immune cells have not been reported yet. In this study we demonstrate that exogenous p41 fragment can enter the endocytic pathway of targeted human immature DC. Internalized p41 fragment has contributed to the total amount of the immunogold labelled p41 Ii-specific epitope, as quantified by transmission electron microscopy, in particular in late endocytic compartments with multivesicular morphology where antigen processing and binding to MHC II take place. In cell lysates of treated immature DC, diminished enzymatic activity of cysteine proteases has been confirmed. Internalized exogenous p41 fragment did not affect the perinuclear clustering of acidic cathepsin S-positive vesicles typical of mature DC. p41 fragment is shown to interfere with the nuclear translocation of NF-κB p65 subunit in LPS-stimulated DC. p41 fragment is also shown to reduce the secretion of interleukin-12 (IL-12/p70) during the subsequent maturation of treated DC. The inhibition of proteolytic activity of lysosomal cysteine proteases in immature DC and the diminished capability of DC to produce IL-12 upon their subsequent maturation support the immunomodulatory potential of the examined thyropin from p41 Ii.
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Affiliation(s)
- Tina Zavašnik-Bergant
- Department of Biochemistry, Molecular and Structural Biology, Jožef Stefan Institute, Ljubljana, Slovenia
- * E-mail:
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41
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Unanue ER, Turk V, Neefjes J. Variations in MHC Class II Antigen Processing and Presentation in Health and Disease. Annu Rev Immunol 2016; 34:265-97. [PMID: 26907214 DOI: 10.1146/annurev-immunol-041015-055420] [Citation(s) in RCA: 170] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
MHC class II (MHC-II) molecules are critical in the control of many immune responses. They are also involved in most autoimmune diseases and other pathologies. Here, we describe the biology of MHC-II and MHC-II variations that affect immune responses. We discuss the classic cell biology of MHC-II and various perturbations. Proteolysis is a major process in the biology of MHC-II, and we describe the various components forming and controlling this endosomal proteolytic machinery. This process ultimately determines the MHC-II-presented peptidome, including cryptic peptides, modified peptides, and other peptides that are relevant in autoimmune responses. MHC-II also variable in expression, glycosylation, and turnover. We illustrate that MHC-II is variable not only in amino acids (polymorphic) but also in its biology, with consequences for both health and disease.
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Affiliation(s)
- Emil R Unanue
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri 63110;
| | - Vito Turk
- Department of Biochemistry and Molecular and Structural Biology, J. Stefan Institute, SI-1000 Ljubljana, Slovenia;
| | - Jacques Neefjes
- Division of Cell Biology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; .,Leiden University Medical Center, 2300 RC Leiden, The Netherlands
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42
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Rajković J, Poreba M, Caglič D, Vidmar R, Wilk A, Borowik A, Salvesen G, Turk V, Drag M, Turk B. Biochemical Characterization and Substrate Specificity of Autophagin-2 from the Parasite Trypanosoma cruzi. J Biol Chem 2015; 290:28231-28244. [PMID: 26446788 DOI: 10.1074/jbc.m115.687764] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Indexed: 12/21/2022] Open
Abstract
The genome of the parasite Trypanosoma cruzi encodes two copies of autophagy-related cysteine proteases, Atg4.1 and Atg4.2. T. cruzi autophagin-2 (TcAtg4.2) carries the majority of proteolytic activity and is responsible for processing Atg8 proteins near the carboxyl terminus, exposing a conserved glycine. This enables progression of autophagy and differentiation of the parasite, which is required for successful colonization of humans. The mechanism of substrate hydrolysis by Atg4 was found to be highly conserved among the species as critical mutations in the TcAtg4.2, including mutation of the conserved Gly-244 residue in the hinge region enabling flexibility of the regulatory loop, and deletion of the regulatory loop, completely abolished processing capacity of the mutants. Using the positional scanning-substrate combinatorial library (PS-SCL) we determined that TcAtg4.2 tolerates a broad spectrum of amino acids in the P4 and P3 positions, similar to the human orthologue autophagin-1 (HsAtg4B). In contrast, both human and trypanosome Atg4 orthologues exhibited exclusive preference for aromatic amino acid residues in the P2 position, and for Gly in the P1 position, which is absolutely conserved in the natural Atg8 substrates. Using an extended P2 substrate library, which also included the unnatural amino acid cyclohexylalanine (Cha) derivative of Phe, we generated highly selective tetrapeptide substrates acetyl-Lys-Lys-Cha-Gly-AFC (Ac-KKChaG-AFC) and acetyl-Lys-Thr-Cha-Gly-AFC (Ac-KTChaG-AFC). Althoughthese substrates were cleaved by cathepsins, making them unsuitable for analysis of complex cellular systems, they were recognized exclusively by TcAtg4.2, but not by HsAtg4B nor by the structurally related human proteases SENP1, SENP2, and UCH-L3.
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Affiliation(s)
- Jelena Rajković
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Jamova Cesta 39, SI-1000 Ljubljana, Slovenia; Jožef Stefan International Postgraduate School, Jamova Cesta 39, SI-1000 Ljubljana, Slovenia
| | - Marcin Poreba
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Dejan Caglič
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Jamova Cesta 39, SI-1000 Ljubljana, Slovenia; Department of Chemistry
| | - Robert Vidmar
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Jamova Cesta 39, SI-1000 Ljubljana, Slovenia; Jožef Stefan International Postgraduate School, Jamova Cesta 39, SI-1000 Ljubljana, Slovenia
| | - Aleksandra Wilk
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Agata Borowik
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Guy Salvesen
- Sanford-Burnham Medical Research Institute, Program in Cell Death and Survival Networks, The Scripps Research Institute, La Jolla, California 92037
| | - Vito Turk
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Jamova Cesta 39, SI-1000 Ljubljana, Slovenia
| | - Marcin Drag
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Boris Turk
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Jamova Cesta 39, SI-1000 Ljubljana, Slovenia; Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova Cesta 39, SI-1000 Ljubljana, Slovenia; Faculty of Chemistry and Chemical Technology, University of Ljubljana, Jamova Cesta 39, SI-1000 Ljubljana, Slovenia.
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Borišek J, Vizovišek M, Sosnowski P, Turk B, Turk D, Mohar B, Novič M. Development of N-(Functionalized benzoyl)-homocycloleucyl-glycinonitriles as Potent Cathepsin K Inhibitors. J Med Chem 2015; 58:6928-37. [PMID: 26280490 DOI: 10.1021/acs.jmedchem.5b00746] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cathepsin K is a major drug target for osteoporosis and related-bone disorders. Using a combination of virtual combinatorial chemistry, QSAR modeling, and molecular docking studies, a series of cathepsin K inhibitors based on N-(functionalized benzoyl)-homocycloleucyl-glycinonitrile scaffold was developed. In order to avoid previous problems of cathepsin K inhibitors associated with lysosomotropism of compounds with basic character that resulted in off-target effects, a weakly- to nonbasic moiety was incorporated into the P3 position. Compounds 5, 6, and 9 were highly selective for cathepsin K when compared with cathepsins L and S, with the Ki values in the 10-30 nM range. The kinetic studies revealed that the new compounds exhibited reversible tight binding to cathepsin K, while the X-ray structural studies showed covalent and noncovalent binding between the nitrile group and the catalytic cysteine (Cys25) site.
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Affiliation(s)
- Jure Borišek
- National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
| | - Matej Vizovišek
- Department of Biochemistry, Molecular and Structural Biology, Jozef Stefan Institute , Jamova cesta 39, SI-1000 Ljubljana, Slovenia
| | - Piotr Sosnowski
- Department of Biochemistry, Molecular and Structural Biology, Jozef Stefan Institute , Jamova cesta 39, SI-1000 Ljubljana, Slovenia
| | - Boris Turk
- Department of Biochemistry, Molecular and Structural Biology, Jozef Stefan Institute , Jamova cesta 39, SI-1000 Ljubljana, Slovenia.,Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova cesta 39, SI-1000 Ljubljana, Slovenia
| | - Dušan Turk
- Department of Biochemistry, Molecular and Structural Biology, Jozef Stefan Institute , Jamova cesta 39, SI-1000 Ljubljana, Slovenia.,Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova cesta 39, SI-1000 Ljubljana, Slovenia.,Faculty of Chemistry and Chemical Technology, University of Ljubljana , Večna pot 113, SI-1000 Ljubljana, Slovenia
| | - Barbara Mohar
- National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
| | - Marjana Novič
- National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
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Sobotič B, Vizovišek M, Vidmar R, Van Damme P, Gocheva V, Joyce JA, Gevaert K, Turk V, Turk B, Fonović M. Proteomic Identification of Cysteine Cathepsin Substrates Shed from the Surface of Cancer Cells. Mol Cell Proteomics 2015; 14:2213-28. [PMID: 26081835 DOI: 10.1074/mcp.m114.044628] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Indexed: 01/08/2023] Open
Abstract
Extracellular cysteine cathepsins are known to drive cancer progression, but besides degradation of extracellular matrix proteins little is known about their physiological substrates and thus the molecular mechanisms they deploy. One of the major mechanisms used by other extracellular proteases to facilitate cancer progression is proteolytic release of the extracellular domains of transmembrane proteins or ectodomain shedding. Here we show using a mass spectrometry-based approach that cathepsins L and S act as sheddases and cleave extracellular domains of CAM adhesion proteins and transmembrane receptors from the surface of cancer cells. In cathepsin S-deficient mouse pancreatic cancers, processing of these cathepsin substrates is highly reduced, pointing to an essential role of cathepsins in extracellular shedding. In addition to influencing cell migration and invasion, shedding of surface proteins by extracellular cathepsins impacts intracellular signaling as demonstrated for regulation of Ras GTPase activity, thereby providing a putative mechanistic link between extracellular cathepsin activity and cancer progression. The MS data is available via ProteomeXchange with identifier PXD002192.
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Affiliation(s)
- Barbara Sobotič
- From the ‡Department of Biochemistry, Molecular and Structural Biology, Jozef Stefan Institute, Jamova cesta 39, SI-1000 Ljubljana, Slovenia; §International Postgraduate School Jozef Stefan, Jamova 39, SI-1000 Ljubljana, Slovenia
| | - Matej Vizovišek
- From the ‡Department of Biochemistry, Molecular and Structural Biology, Jozef Stefan Institute, Jamova cesta 39, SI-1000 Ljubljana, Slovenia; §International Postgraduate School Jozef Stefan, Jamova 39, SI-1000 Ljubljana, Slovenia
| | - Robert Vidmar
- From the ‡Department of Biochemistry, Molecular and Structural Biology, Jozef Stefan Institute, Jamova cesta 39, SI-1000 Ljubljana, Slovenia; §International Postgraduate School Jozef Stefan, Jamova 39, SI-1000 Ljubljana, Slovenia
| | - Petra Van Damme
- ¶Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium; ‖Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium
| | - Vasilena Gocheva
- **Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065
| | - Johanna A Joyce
- **Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065
| | - Kris Gevaert
- ¶Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium; ‖Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium
| | - Vito Turk
- From the ‡Department of Biochemistry, Molecular and Structural Biology, Jozef Stefan Institute, Jamova cesta 39, SI-1000 Ljubljana, Slovenia; §International Postgraduate School Jozef Stefan, Jamova 39, SI-1000 Ljubljana, Slovenia; ‡‡Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova cesta 39, SI-1000 Ljubljana, Slovenia
| | - Boris Turk
- From the ‡Department of Biochemistry, Molecular and Structural Biology, Jozef Stefan Institute, Jamova cesta 39, SI-1000 Ljubljana, Slovenia; ‡‡Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova cesta 39, SI-1000 Ljubljana, Slovenia; §§Center of Excellence NIN, Ljubljana, Slovenia; ¶¶Faculty of Chemistry and Chemical Technology, University of Ljubljana, Slovenia
| | - Marko Fonović
- From the ‡Department of Biochemistry, Molecular and Structural Biology, Jozef Stefan Institute, Jamova cesta 39, SI-1000 Ljubljana, Slovenia; ‡‡Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova cesta 39, SI-1000 Ljubljana, Slovenia;
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Yang Y, Duan JZ, Di Y, Gui DM, Gao DW. Bioinformatics analysis of potential essential genes that response to the high intraocular pressure on astrocyte due to glaucoma. Int J Ophthalmol 2015; 8:395-8. [PMID: 25938062 DOI: 10.3980/j.issn.2222-3959.2015.02.32] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 08/22/2014] [Indexed: 11/02/2022] Open
Abstract
AIM To study the gene expression response and predict the network in cell due to pressure effects on optic nerve injury of glaucoma. METHODS We used glaucoma related microarray data in public database [Gene Expression Omnibus (GEO)] to explore the potential gene expression changes as well as correspondent biological process alterations due to increased pressure in astrocytes during glaucoma development. RESULTS A total of six genes were identified to be related with pressure increasing. Through the annotation and network analysis, we found these genes might be involved in cell morphological remodeling, angiogenesis, mismatch repair. CONCLUSION Increasing pressure in glaucoma on astrocytes might cause gene expression alterations, which might induce some cellular responses changes.
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Affiliation(s)
- Yang Yang
- Department of Ophthalmology, China Medical University, Shengjing Hospital, Shenyang 110004, Liaoning Province, China
| | - Jing-Zhu Duan
- Department of Orthopedics, China Medical University, Shengjing Hospital, Shenyang 110004, Liaoning Province, China
| | - Yu Di
- Department of Ophthalmology, China Medical University, Shengjing Hospital, Shenyang 110004, Liaoning Province, China
| | - Dong-Mei Gui
- Department of Ophthalmology, China Medical University, Shengjing Hospital, Shenyang 110004, Liaoning Province, China
| | - Dian-Wen Gao
- Department of Ophthalmology, China Medical University, Shengjing Hospital, Shenyang 110004, Liaoning Province, China
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46
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Ben-Nun Y, Merquiol E, Brandis A, Turk B, Scherz A, Blum G. Photodynamic quenched cathepsin activity based probes for cancer detection and macrophage targeted therapy. Theranostics 2015; 5:847-62. [PMID: 26000057 PMCID: PMC4440442 DOI: 10.7150/thno.10854] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 03/20/2015] [Indexed: 11/10/2022] Open
Abstract
Elevated cathepsins levels and activities are found in several types of human cancer, making them valuable biomarkers for detection and targeting therapeutics. We designed small molecule quenched activity-based probes (qABPs) that fluoresce upon activity-dependent covalent modification, yielding cell killing by Photodynamic Therapy (PDT). These novel molecules are highly selective theranostic probes that enable both detection and treatment of cancer with minimal side effects. Our qABPs carry a photosensitizer (PS), which is activated by light, resulting in oxidative stress and subsequent cell ablation, and a quencher that when removed by active cathepsins allow the PS to fluoresce and demonstrate PD properties. Our most powerful and stable PS-qABP, YBN14, consists of a selective cathepsin recognition sequence, a QC-1 quencher and a new bacteriochlorin derivative as a PS. YBN14 allowed rapid and selective non-invasive in vivo imaging of subcutaneous tumors and induced specific tumor macrophage apoptosis by light treatment, resulting in a substantial tumor shrinkage in an aggressive breast cancer mouse model. These results demonstrate for the first time that the PS-qABPs technology offers a functional theranostic tool, which can be applied to numerous tumor types and other inflammation-associated diseases.
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Affiliation(s)
- Yael Ben-Nun
- 1. The Institute of Drug Research, The School of Pharmacy, The Faculty of Medicine, Campus Ein Karem, The Hebrew University, Jerusalem, Israel
| | - Emmanuelle Merquiol
- 1. The Institute of Drug Research, The School of Pharmacy, The Faculty of Medicine, Campus Ein Karem, The Hebrew University, Jerusalem, Israel
| | - Alexander Brandis
- 2. Department of Plant Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Boris Turk
- 3. Department of Biochemistry and Molecular Biology, J. Stefan Institute, Ljubljana, Slovenia
- 4. Faculty of Chemistry and Chemical Technology, University of Ljubljana, Slovenia
- 5. Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Ljubljana, Slovenia
| | - Avigdor Scherz
- 2. Department of Plant Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Galia Blum
- 1. The Institute of Drug Research, The School of Pharmacy, The Faculty of Medicine, Campus Ein Karem, The Hebrew University, Jerusalem, Israel
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47
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Repnik U, Starr AE, Overall CM, Turk B. Cysteine Cathepsins Activate ELR Chemokines and Inactivate Non-ELR Chemokines. J Biol Chem 2015; 290:13800-11. [PMID: 25833952 DOI: 10.1074/jbc.m115.638395] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Indexed: 12/24/2022] Open
Abstract
Cysteine cathepsins are primarily lysosomal proteases involved in general protein turnover, but they also have specific proteolytic functions in antigen presentation and bone remodeling. Cathepsins are most stable at acidic pH, although growing evidence indicates that they have physiologically relevant activity also at neutral pH. Post-translational proteolytic processing of mature chemokines is a key, yet underappreciated, level of chemokine regulation. Although the role of selected serine proteases and matrix metalloproteases in chemokine processing has long been known, little has been reported about the role of cysteine cathepsins. Here we evaluated cleavage of CXC ELR (CXCL1, -2, -3, -5, and -8) and non-ELR (CXCL9-12) chemokines by cysteine cathepsins B, K, L, and S at neutral pH by high resolution Tris-Tricine SDS-PAGE and matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Whereas cathepsin B cleaved chemokines especially in the C-terminal region, cathepsins K, L, and S cleaved chemokines at the N terminus with glycosaminoglycans modulating cathepsin processing of chemokines. The functional consequences of the cleavages were determined by Ca(2+) mobilization and chemotaxis assays. We show that cysteine cathepsins inactivate and in some cases degrade non-ELR CXC chemokines CXCL9-12. In contrast, cathepsins specifically process ELR CXC chemokines CXCL1, -2, -3, -5, and -8 N-terminally to the ELR motif, thereby generating agonist forms. This study suggests that cysteine cathepsins regulate chemokine activity and thereby leukocyte recruitment during protective or pathological inflammation.
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Affiliation(s)
- Urska Repnik
- From the Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, SI-1000 Ljubljana, Slovenia
| | - Amanda E Starr
- the Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Christopher M Overall
- the Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada, the Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada,
| | - Boris Turk
- From the Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, SI-1000 Ljubljana, Slovenia, the Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, SI-1000 Ljubljana, Slovenia, and the Faculty of Chemistry and Chemical Technology, University of Ljubljana, SI-1000 Ljubljana, Slovenia
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48
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Vizovišek M, Vidmar R, Van Quickelberghe E, Impens F, Andjelković U, Sobotič B, Stoka V, Gevaert K, Turk B, Fonović M. Fast profiling of protease specificity reveals similar substrate specificities for cathepsins K, L and S. Proteomics 2015; 15:2479-90. [PMID: 25626674 DOI: 10.1002/pmic.201400460] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 12/02/2014] [Accepted: 01/22/2015] [Indexed: 11/12/2022]
Abstract
Proteases are important effectors of numerous physiological and pathological processes. Reliable determination of a protease's specificity is crucial to understand protease function and to develop activity-based probes and inhibitors. During the last decade, various proteomic approaches for profiling protease substrate specificities were reported. Although most of these approaches can identify up to thousands of substrate cleavage events in a single experiment, they are often time consuming and methodologically challenging as some of these approaches require rather complex sample preparation procedures. For such reasons their application is often limited to those labs that initially introduced them. Here, we report on a fast and simple approach for proteomic profiling of protease specificities (fast profiling of protease specificity (FPPS)), which can be applied to complex protein mixtures. FPPS is based on trideutero-acetylation of novel N-termini generated by the action of proteases and subsequent peptide fractionation on Stage Tips containing ion-exchange and reverse phase chromatographic resins. FPPS can be performed in 2 days and does not require extensive fractionation steps. Using this approach, we have determined the specificity profiles of the cysteine cathepsins K, L and S. We further validated our method by comparing the results with the specificity profiles obtained by the N-terminal combined fractional diagonal chromatography method. This comparison pointed to almost identical substrate specificities for all three cathepsins and confirmed the reliability of the FPPS approach. All MS data have been deposited in the ProteomeXchange with identifiers PXD001536 and PXD001553 (http://proteomecentral.proteomexchange.org/dataset/PXD001536; http://proteomecentral.proteomexchange.org/dataset/PXD001553).
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Affiliation(s)
- Matej Vizovišek
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Ljubljana, Slovenia.,Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Ljubljana, Slovenia.,International Postgraduate School Jozef Stefan, Ljubljana, Slovenia
| | - Robert Vidmar
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Ljubljana, Slovenia.,International Postgraduate School Jozef Stefan, Ljubljana, Slovenia
| | - Emmy Van Quickelberghe
- Department of Biochemistry, Ghent University, Ghent, Belgium.,Department of Medical Protein Research, Ghent, Belgium
| | - Francis Impens
- Department of Biochemistry, Ghent University, Ghent, Belgium.,Department of Medical Protein Research, Ghent, Belgium.,Unité des Interactions Bactéries-Cellules, Institut Pasteur, Paris, France
| | - Uroš Andjelković
- Department of Chemistry, Institute of Chemistry, Technology and Metallurgy, University of Belgrade, Belgrade, Serbia
| | - Barbara Sobotič
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Ljubljana, Slovenia.,International Postgraduate School Jozef Stefan, Ljubljana, Slovenia
| | - Veronika Stoka
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Ljubljana, Slovenia
| | - Kris Gevaert
- Department of Biochemistry, Ghent University, Ghent, Belgium.,Department of Medical Protein Research, Ghent, Belgium
| | - Boris Turk
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Ljubljana, Slovenia.,Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Ljubljana, Slovenia.,Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | - Marko Fonović
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Ljubljana, Slovenia.,Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Ljubljana, Slovenia
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49
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The human-specific invariant chain isoform Iip35 modulates Iip33 trafficking and function. Immunol Cell Biol 2014; 92:791-8. [PMID: 24983457 DOI: 10.1038/icb.2014.54] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Revised: 05/12/2014] [Accepted: 05/31/2014] [Indexed: 12/24/2022]
Abstract
The invariant chain (Ii) is a multifunctional protein, which has an essential role in the assembly and transport of major histocompatibility complex class II (MHC II) molecules. From a single gene, Ii is synthesized as four different isoforms: Iip33, Iip35, Iip41 and Iip43. Iip35 and Iip43 are specific to humans, and are formed due to an upstream alternative translation site, resulting in an N-terminal extension of 16 amino acids. This extension harbors a strong endoplasmic reticulum (ER) retention motif. Consequently, Iip35 or Iip43 expressed alone are retained in the ER, whereas Iip33 and Iip41 rapidly traffic to the endosomal pathway. Endogenously expressed, the four isoforms form mixed heterotrimers in the ER; however, mainly due to the absence of the Iip35/p43 isoforms in mice, little is known about how they influence general Ii function. In this study, we have co-expressed Iip33 and Iip35 in human cells with and without MHC II to gain a better understanding of how Iip35 isoform influences the cellular properties of Iip33. We find that Iip35 significantly affects the properties of Iip33. In the presence of Iip35, the transport of Iip33 out of the ER is delayed, its half-life is dramatically prolonged and its ability to induce enlarged endosomes and delayed endosomal maturation is abrogated.
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50
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Fortin JS, Cloutier M, Thibodeau J. Exposing the Specific Roles of the Invariant Chain Isoforms in Shaping the MHC Class II Peptidome. Front Immunol 2013; 4:443. [PMID: 24379812 PMCID: PMC3861868 DOI: 10.3389/fimmu.2013.00443] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 11/26/2013] [Indexed: 11/26/2022] Open
Abstract
The peptide repertoire (peptidome) associated with MHC class II molecules (MHCIIs) is influenced by the polymorphic nature of the peptide binding groove but also by cell-intrinsic factors. The invariant chain (Ii) chaperones MHCIIs, affecting their folding and trafficking. Recent discoveries relating to Ii functions have provided insights as to how it edits the MHCII peptidome. In humans, the Ii gene encodes four different isoforms for which structure-function analyses have highlighted common properties but also some non-redundant roles. Another layer of complexity arises from the fact that Ii heterotrimerizes, a characteristic that has the potential to affect the maturation of associated MHCIIs in many different ways, depending on the isoform combinations. Here, we emphasize the peptide editing properties of Ii and discuss the impact of the various isoforms on the MHCII peptidome.
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Affiliation(s)
- Jean-Simon Fortin
- Laboratoire d'Immunologie Moléculaire, Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal , Montréal, QC , Canada
| | - Maryse Cloutier
- Laboratoire d'Immunologie Moléculaire, Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal , Montréal, QC , Canada
| | - Jacques Thibodeau
- Laboratoire d'Immunologie Moléculaire, Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal , Montréal, QC , Canada
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