1
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Xu B, Anderson BM, Mountford SJ, Thompson PE, Mintern JD, Edgington-Mitchell LE. Cathepsin X deficiency alters the processing and localisation of cathepsin L and impairs cleavage of a nuclear cathepsin L substrate. Biol Chem 2024; 405:351-365. [PMID: 38410910 DOI: 10.1515/hsz-2023-0355] [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: 11/29/2023] [Accepted: 02/12/2024] [Indexed: 02/28/2024]
Abstract
Proteases function within sophisticated networks. Altering the activity of one protease can have sweeping effects on other proteases, leading to changes in their activity, structure, specificity, localisation, stability, and expression. Using a suite of chemical tools, we investigated the impact of cathepsin X, a lysosomal cysteine protease, on the activity and expression of other cysteine proteases and their inhibitors in dendritic cells. Among all proteases examined, cathepsin X gene deletion specifically altered cathepsin L levels; pro-cathepsin L and its single chain accumulated while the two-chain form was unchanged. This effect was recapitulated by chemical inhibition of cathepsin X, suggesting a dependence on its catalytic activity. We demonstrated that accumulation of pro- and single chain cathepsin L was not due to a lack of direct cleavage by cathepsin X or altered glycosylation, secretion, or mRNA expression but may result from changes in lysosomal oxidative stress or pH. In the absence of active cathepsin X, nuclear cathepsin L and cleavage of the known nuclear cathepsin L substrate, Lamin B1, were diminished. Thus, cathepsin X activity selectively regulates cathepsin L, which has the potential to impact the degree of cathepsin L proteolysis, the nature of substrates that it cleaves, and the location of cleavage.
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Affiliation(s)
- Bangyan Xu
- Department of Biochemistry & Pharmacology, 2281 Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne , Parkville, VIC 3052, Australia
| | - Bethany M Anderson
- Department of Biochemistry & Pharmacology, 2281 Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne , Parkville, VIC 3052, Australia
| | - Simon J Mountford
- Medicinal Chemistry, 2541 Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, VIC 3052, Australia
| | - Philip E Thompson
- Medicinal Chemistry, 2541 Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, VIC 3052, Australia
| | - Justine D Mintern
- Department of Biochemistry & Pharmacology, 2281 Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne , Parkville, VIC 3052, Australia
| | - Laura E Edgington-Mitchell
- Department of Biochemistry & Pharmacology, 2281 Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne , Parkville, VIC 3052, Australia
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2
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Ziegler AR, Dufour A, Scott NE, Edgington-Mitchell LE. Ion Mobility-Based Enrichment-Free N-Terminomics Analysis Reveals Novel Legumain Substrates in Murine Spleen. Mol Cell Proteomics 2024; 23:100714. [PMID: 38199506 PMCID: PMC10862022 DOI: 10.1016/j.mcpro.2024.100714] [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: 07/28/2023] [Revised: 12/19/2023] [Accepted: 01/02/2024] [Indexed: 01/12/2024] Open
Abstract
Aberrant levels of the asparaginyl endopeptidase legumain have been linked to inflammation, neurodegeneration, and cancer, yet our understanding of this protease is incomplete. Systematic attempts to identify legumain substrates have been previously confined to in vitro studies, which fail to mirror physiological conditions and obscure biologically relevant cleavage events. Using high-field asymmetric waveform ion mobility spectrometry (FAIMS), we developed a streamlined approach for proteome and N-terminome analyses without the need for N-termini enrichment. Compared to unfractionated proteomic analysis, we demonstrate FAIMS fractionation improves N-termini identification by >2.5 fold, resulting in the identification of >2882 unique N-termini from limited sample amounts. In murine spleens, this approach identifies 6366 proteins and 2528 unique N-termini, with 235 cleavage events enriched in WT compared to legumain-deficient spleens. Among these, 119 neo-N-termini arose from asparaginyl endopeptidase activities, representing novel putative physiological legumain substrates. The direct cleavage of selected substrates by legumain was confirmed using in vitro assays, providing support for the existence of physiologically relevant extra-lysosomal legumain activity. Combined, these data shed critical light on the functions of legumain and demonstrate the utility of FAIMS as an accessible method to improve depth and quality of N-terminomics studies.
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Affiliation(s)
- Alexander R Ziegler
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Antoine Dufour
- Department of Physiology and Pharmacology, University of Calgary, Calgary, Alberta, Canada; McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, Alberta, Canada
| | - Nichollas E Scott
- Department of Microbiology and Immunology, Peter Doherty Institute, The University of Melbourne, Parkville, Victoria, Australia.
| | - Laura E Edgington-Mitchell
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia.
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3
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Das N, de Almeida LGN, Derakhshani A, Young D, Mehdinejadiani K, Salo P, Rezansoff A, Jay GD, Sommerhoff CP, Schmidt TA, Krawetz R, Dufour A. Tryptase β regulation of joint lubrication and inflammation via proteoglycan-4 in osteoarthritis. Nat Commun 2023; 14:1910. [PMID: 37024468 PMCID: PMC10079686 DOI: 10.1038/s41467-023-37598-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 03/09/2023] [Indexed: 04/08/2023] Open
Abstract
PRG4 is an extracellular matrix protein that maintains homeostasis through its boundary lubricating and anti-inflammatory properties. Altered expression and function of PRG4 have been associated with joint inflammatory diseases, including osteoarthritis. Here we show that mast cell tryptase β cleaves PRG4 in a dose- and time-dependent manner, which was confirmed by silver stain gel electrophoresis and mass spectrometry. Tryptase-treated PRG4 results in a reduction of lubrication. Compared to full-length, cleaved PRG4 further activates NF-κB expression in cells overexpressing TLR2, -4, and -5. In the destabilization of the medial meniscus model of osteoarthritis in rat, tryptase β and PRG4 colocalize at the site of injury in knee cartilage and is associated with disease severity. When human primary synovial fibroblasts from male osteoarthritis patients or male healthy subjects treated with tryptase β and/or PRG4 are subjected to a quantitative shotgun proteomics and proteome changes are characterized, it further supports the role of NF-κB activation. Here we show that tryptase β as a modulator of joint lubrication in osteoarthritis via the cleavage of PRG4.
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Affiliation(s)
- Nabangshu Das
- Faculty of Kinesiology, University of Calgary, Calgary, AB, Canada
- Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- McCaig Institute for Bone and Joint Health, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Luiz G N de Almeida
- Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- McCaig Institute for Bone and Joint Health, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Afshin Derakhshani
- Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- McCaig Institute for Bone and Joint Health, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Daniel Young
- Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- McCaig Institute for Bone and Joint Health, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Kobra Mehdinejadiani
- Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- McCaig Institute for Bone and Joint Health, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Paul Salo
- McCaig Institute for Bone and Joint Health, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Alexander Rezansoff
- Faculty of Kinesiology, University of Calgary, Calgary, AB, Canada
- McCaig Institute for Bone and Joint Health, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Gregory D Jay
- Department of Emergency Medicine, Warren Alpert Medical School & School of Engineering, Brown University, Providence, RI, USA
| | - Christian P Sommerhoff
- Institute of Medical Education and Institute of Laboratory Medicine, University Hospital, LMU Munich, Munich, Germany
| | - Tannin A Schmidt
- McCaig Institute for Bone and Joint Health, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Biomedical Engineering Department, University of Connecticut Health Center, Farmington, CT, USA
| | - Roman Krawetz
- McCaig Institute for Bone and Joint Health, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
- Cell Biology and Anatomy, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
| | - Antoine Dufour
- Faculty of Kinesiology, University of Calgary, Calgary, AB, Canada.
- Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
- McCaig Institute for Bone and Joint Health, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
- Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
- Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
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4
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The Asparaginyl Endopeptidase Legumain: An Emerging Therapeutic Target and Potential Biomarker for Alzheimer’s Disease. Int J Mol Sci 2022; 23:ijms231810223. [PMID: 36142134 PMCID: PMC9499314 DOI: 10.3390/ijms231810223] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 08/30/2022] [Accepted: 09/02/2022] [Indexed: 11/21/2022] Open
Abstract
Alzheimer’s disease (AD) is incurable dementia closely associated with aging. Most cases of AD are sporadic, and very few are inherited; the pathogenesis of sporadic AD is complex and remains to be elucidated. The asparaginyl endopeptidase (AEP) or legumain is the only recognized cysteine protease that specifically hydrolyzes peptide bonds after asparagine residues in mammals. The expression level of AEPs in healthy brains is far lower than that of peripheral organs. Recently, growing evidence has indicated that aging may upregulate and overactivate brain AEPs. The overactivation of AEPs drives the onset of AD through cleaving tau and amyloid precursor proteins (APP), and SET, an inhibitor of protein phosphatase 2A (PP2A). The AEP-mediated cleavage of these peptides enhances amyloidosis, promotes tau hyperphosphorylation, and ultimately induces neurodegeneration and cognitive impairment. Upregulated AEPs and related deleterious reactions constitute upstream events of amyloid/tau toxicity in the brain, and represent early pathological changes in AD. Thus, upregulated AEPs are an emerging drug target for disease modification and a potential biomarker for predicting preclinical AD. However, the presence of the blood–brain barrier greatly hinders establishing body-fluid-based methods to measure brain AEPs. Research on AEP-activity-based imaging probes and our recent work suggest that the live brain imaging of AEPs could be used to evaluate its predictive efficacy as an AD biomarker. To advance translational research in this area, AEP imaging probes applicable to human brain and AEP inhibitors with good druggability are urgently needed.
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5
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Uzozie AC, Smith TG, Chen S, Lange PF. Sensitive Identification of Known and Unknown Protease Activities by Unsupervised Linear Motif Deconvolution. Anal Chem 2022; 94:2244-2254. [PMID: 35029975 DOI: 10.1021/acs.analchem.1c04937] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The cleavage-site specificities for many proteases are not well understood, restricting the utility of supervised classification methods. We present an algorithm and web interface to overcome this limitation through the unsupervised detection of overrepresented patterns in protein sequence data, providing insight into the mixture of protease activities contributing to a complex system. Here, we apply the RObust LInear Motif Deconvolution (RoLiM) algorithm to confidently detect substrate cleavage patterns for SARS-CoV-2 MPro protease in the N-terminome data of an infected human cell line. Using mass spectrometry-based peptide data from a case-control comparison of 341 primary urothelial bladder cancer cases and 110 controls, we identified distinct sequence motifs indicative of increased matrix metallopeptidase activity in urine from cancer patients. The evaluation of N-terminal peptides from patient plasma post-chemotherapy detected novel granzyme B/corin activity. RoLiM will enhance the unbiased investigation of peptide sequences to establish the composition of known and uncharacterized protease activities in biological systems. RoLiM is available at http://langelab.org/rolim/.
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Affiliation(s)
- Anuli C Uzozie
- Department of Pathology, University of British Columbia, Vancouver, British Columbia V6T 1Z7, Canada.,Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital Research Institute, Vancouver, British Columbia V5Z 4H4, Canada
| | - Theodore G Smith
- Department of Pathology, University of British Columbia, Vancouver, British Columbia V6T 1Z7, Canada.,Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital Research Institute, Vancouver, British Columbia V5Z 4H4, Canada
| | - Siyuan Chen
- Department of Pathology, University of British Columbia, Vancouver, British Columbia V6T 1Z7, Canada.,Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital Research Institute, Vancouver, British Columbia V5Z 4H4, Canada
| | - Philipp F Lange
- Department of Pathology, University of British Columbia, Vancouver, British Columbia V6T 1Z7, Canada.,Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital Research Institute, Vancouver, British Columbia V5Z 4H4, Canada.,Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia V5Z 1L3, Canada
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6
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Anowai A, Chopra S, Mainoli B, Young D, Dufour A. N-Terminomics/TAILS of Tissue and Liquid Biopsies. Methods Mol Biol 2022; 2456:85-94. [PMID: 35612737 DOI: 10.1007/978-1-0716-2124-0_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The N-terminomics approach of Terminal Amine Isotopic Labeling of Substrates (TAILS) enables the identification and quantification of natural and neo-N-termini of proteins using liquid chromatography and tandem mass spectrometry (LC-MS/MS). This methodology has been used to study protease function and identify protease substrates in cell culture systems, animal disease models, and more recently, has been applied to clinical samples. Here, we present the application of TAILS to tissue and liquid biopsies.
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Affiliation(s)
- Anthonia Anowai
- Department of Physiology and Pharmacology, University of Calgary, Calgary, AB, Canada
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada
- McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, AB, Canada
- Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada
| | - Sameeksha Chopra
- Department of Physiology and Pharmacology, University of Calgary, Calgary, AB, Canada
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada
- McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, AB, Canada
- Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada
| | - Barbara Mainoli
- Department of Physiology and Pharmacology, University of Calgary, Calgary, AB, Canada
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada
- McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, AB, Canada
- Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada
| | - Daniel Young
- Department of Physiology and Pharmacology, University of Calgary, Calgary, AB, Canada
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada
- McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, AB, Canada
- Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada
| | - Antoine Dufour
- Department of Physiology and Pharmacology, University of Calgary, Calgary, AB, Canada.
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada.
- McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, AB, Canada.
- Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada.
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7
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Kim ML, Hardy MY, Edgington-Mitchell LE, Ramarathinam SH, Chung SZ, Russell AK, Currie I, Sleebs BE, Purcell AW, Tye-Din JA, Wicks IP. Hydroxychloroquine inhibits the mitochondrial antioxidant system in activated T cells. iScience 2021; 24:103509. [PMID: 34934928 DOI: 10.1016/j.isci.2021.103509] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 10/15/2021] [Accepted: 11/20/2021] [Indexed: 12/30/2022] Open
Abstract
Although hydroxychloroquine (HCQ) has long been used to treat autoimmune diseases, its mechanism of action remains poorly understood. In CD4 T-cells, we found that a clinically relevant concentration of HCQ inhibited the mitochondrial antioxidant system triggered by TCR crosslinking, leading to increased mitochondrial superoxide, impaired activation-induced autophagic flux, and reduced proliferation of CD4 T-cells. In antigen-presenting cells, HCQ also reduced constitutive activation of the endo-lysosomal protease legumain and toll-like receptor 9, thereby reducing cytokine production, but it had little apparent impact on constitutive antigen processing and peptide presentation. HCQ's effects did not require endo-lysosomal pH change, nor impaired autophagosome-lysosome fusion. We explored the clinical relevance of these findings in patients with celiac disease-a prototypic CD4 T-cell-mediated disease-and found that HCQ limits ex vivo antigen-specific T cell responses. We report a T-cell-intrinsic immunomodulatory effect from HCQ and suggest potential re-purposing of HCQ for celiac disease.
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Affiliation(s)
- Man Lyang Kim
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Melinda Y Hardy
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Laura E Edgington-Mitchell
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3052, Australia.,Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia.,Department of Oral and Maxillofacial Surgery, New York University College of Dentistry, Bluestone Center for Clinical Research, New York, NY 10010, USA
| | - Sri H Ramarathinam
- Infection and Immunity Program and The Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute Monash University, Clayton, VIC 3800, Australia
| | - Shan Zou Chung
- Infection and Immunity Program and The Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute Monash University, Clayton, VIC 3800, Australia
| | - Amy K Russell
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Iain Currie
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Brad E Sleebs
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Anthony W Purcell
- Infection and Immunity Program and The Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute Monash University, Clayton, VIC 3800, Australia
| | - Jason A Tye-Din
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia.,Gastroenterology Department, Royal Melbourne Hospital, Parkville, VIC 3052, Australia
| | - Ian P Wicks
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia.,Rheumatology Unit, Royal Melbourne Hospital, Parkville, VIC 3052, Australia
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8
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Das N, Menon NG, de Almeida LGN, Woods PS, Heynen ML, Jay GD, Caffery B, Jones L, Krawetz R, Schmidt TA, Dufour A. Proteomics Analysis of Tears and Saliva From Sjogren's Syndrome Patients. Front Pharmacol 2021; 12:787193. [PMID: 34950038 PMCID: PMC8689002 DOI: 10.3389/fphar.2021.787193] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/02/2021] [Indexed: 12/17/2022] Open
Abstract
Sjogren's syndrome (SS) is characterized by dysfunctional mucous membranes and dysregulated moisture-secreting glands resulting in various symptoms, including dry mouth and dry eyes. Here, we wanted to profile and compare the tear and saliva proteomes of SS patients to healthy controls. Tear and saliva samples were collected and subjected to an isotopic dimethylation labeling shotgun proteomics workflow to identify alterations in protein levels. In tear samples, we identified 83 upregulated and 112 downregulated proteins. Pathway enrichment analysis of the changing proteins by Metascape identified leukocyte transendothelial migration, neutrophil degranulation, and post-translation protein phosphorylation in tears of SS patients. In healthy controls' tears, an enrichment for proteins related to glycolysis, amino acid metabolism and apoptotic signaling pathway were identified. In saliva, we identified 108 upregulated and 45 downregulated proteins. Altered pathways in SS patients' saliva included cornification, sensory perception to taste and neutrophil degranulation. In healthy controls' saliva, an enrichment for proteins related to JAK-STAT signaling after interleukin-12 stimulation, phagocytosis and glycolysis in senescence were identified. Dysregulated protease activity is implicated in the initiation of inflammation and immune cell recruitment in SS. We identified 20 proteases and protease inhibitors in tears and 18 in saliva which are differentially expressed between SS patients and healthy controls. Next, we quantified endogenous proteoglycan 4 (PRG4), a mucin-like glycoprotein, in tear wash and saliva samples via a bead-based immune assay. We identified decreased levels of PRG4 in SS patients' tear wash compared to normal samples. Conversely, in saliva, we found elevated levels of PRG4 concentration and visualized PRG4 expression in human parotid gland via immunohistological staining. These findings will improve our mechanistic understanding of the disease and changes in SS patients' protein expression will help identify new potential drug targets. PRG4 is among the promising targets, which we identified here, in saliva, for the first time.
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Affiliation(s)
- Nabangshu Das
- Departments of Physiology and Pharmacology and Kinesiology, University of Calgary, Calgary, AB, Canada
- McCaig Institute, University of Calgary, Calgary, AB, Canada
| | - Nikhil G. Menon
- Department of Biomedical Engineering, School of Dental Medicine, UConn Health, Farmington, CT, United States
| | - Luiz G. N. de Almeida
- Departments of Physiology and Pharmacology and Kinesiology, University of Calgary, Calgary, AB, Canada
- McCaig Institute, University of Calgary, Calgary, AB, Canada
| | - Paige S. Woods
- Department of Emergency Medicine, Warren Alpert Medical School and School of Engineering, Brown University, Providence, RI, United States
| | - Miriam L. Heynen
- Centre for Ocular Research and Education (CORE), School of Optometry and Vision Science, University of Waterloo, Waterloo, ON, Canada
| | - Gregory D. Jay
- Department of Emergency Medicine, Warren Alpert Medical School and School of Engineering, Brown University, Providence, RI, United States
| | | | - Lyndon Jones
- Centre for Ocular Research and Education (CORE), School of Optometry and Vision Science, University of Waterloo, Waterloo, ON, Canada
| | - Roman Krawetz
- McCaig Institute, University of Calgary, Calgary, AB, Canada
- Department of Cell Biology and Anatomy, University of Calgary, Calgary, AB, Canada
| | - Tannin A. Schmidt
- McCaig Institute, University of Calgary, Calgary, AB, Canada
- Department of Biomedical Engineering, School of Dental Medicine, UConn Health, Farmington, CT, United States
| | - Antoine Dufour
- Departments of Physiology and Pharmacology and Kinesiology, University of Calgary, Calgary, AB, Canada
- McCaig Institute, University of Calgary, Calgary, AB, Canada
- Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada
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9
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Abstract
All living organisms depend on tightly regulated cellular networks to control biological functions. Proteolysis is an important irreversible post-translational modification that regulates most, if not all, cellular processes. Proteases are a large family of enzymes that perform hydrolysis of protein substrates, leading to protein activation or degradation. The 473 known and 90 putative human proteases are divided into 5 main mechanistic groups: metalloproteases, serine proteases, cysteine proteases, threonine proteases, and aspartic acid proteases. Proteases are fundamental to all biological systems, and when dysregulated they profoundly influence disease progression. Inhibiting proteases has led to effective therapies for viral infections, cardiovascular disorders, and blood coagulation just to name a few. Between 5 and 10% of all pharmaceutical targets are proteases, despite limited knowledge about their biological roles. More than 50% of all human proteases have no known substrates. We present here a comprehensive list of all current known human proteases. We also present current and novel biochemical tools to characterize protease functions in vitro, in vivo, and ex vivo. These tools make it achievable to define both beneficial and detrimental activities of proteases in health and disease.
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Affiliation(s)
- Longxiang Wang
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Kimberly Main
- Department of Physiology & Pharmacology, University of Calgary, Calgary, AB T2N 1N4, Canada.,McCaig Institute for Bone & Joint Health, University of Calgary, Calgary, AB T2N 1N4, Canada.,Hotchkiss Brain Institute, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Henry Wang
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Olivier Julien
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Antoine Dufour
- Department of Physiology & Pharmacology, University of Calgary, Calgary, AB T2N 1N4, Canada.,McCaig Institute for Bone & Joint Health, University of Calgary, Calgary, AB T2N 1N4, Canada.,Hotchkiss Brain Institute, University of Calgary, Calgary, AB T2N 1N4, Canada
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10
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Begum S, Moreau F, Dufour A, Chadee K. Entamoeba histolytica exploits the autophagy pathway in macrophages to trigger inflammation in disease pathogenesis. Mucosal Immunol 2021; 14:1038-1054. [PMID: 33963264 DOI: 10.1038/s41385-021-00408-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 03/25/2021] [Accepted: 04/16/2021] [Indexed: 02/04/2023]
Abstract
The mechanism whereby Entamoeba histolytica (Eh) binding with macrophages at the intercellular junction triggers aggressive pro-inflammatory responses in disease pathogenesis is not well understood. The host intracellular protein degradation process autophagy and its regulatory proteins are involved in maintenance of cellular homeostasis and excessive inflammatory responses. In this study we unraveled how Eh hijacks the autophagy process in macrophages to dysregulate pro-inflammatory responses. Direct contact of live Eh with macrophages activated caspase-6 that induced rapid proteolytic degradation of the autophagy ATG16L1 protein complex independent of NLRP3 inflammasome and caspase-3/8 activation. Crohn's disease susceptible ATG16L1 T300A variant was highly susceptible to Eh-mediated degradation that augmented pro-inflammatory cytokines in mice. Quantitative proteomics revealed downregulation of autophagy and vesicle-mediated transport and upregulation of cysteine-type endopeptidase pathways in response to Eh. We conclude during Eh-macrophage outside-in signaling, ATG16L1 protein complex plays an overlooked regulatory role in shaping the pro-inflammatory landscape in amebiasis.
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Affiliation(s)
- Sharmin Begum
- Departments of Microbiology, Immunology and Infectious Diseases, Calgary, AB, Canada
| | - France Moreau
- Departments of Microbiology, Immunology and Infectious Diseases, Calgary, AB, Canada
| | - Antoine Dufour
- Physiology and Pharmacology, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada.,Biochemistry and Molecular Biology, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada
| | - Kris Chadee
- Departments of Microbiology, Immunology and Infectious Diseases, Calgary, AB, Canada.
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Juurikka K, Dufour A, Pehkonen K, Mainoli B, Campioni Rodrigues P, Solis N, Klein T, Nyberg P, Overall CM, Salo T, Åström P. MMP8 increases tongue carcinoma cell-cell adhesion and diminishes migration via cleavage of anti-adhesive FXYD5. Oncogenesis 2021; 10:44. [PMID: 34059618 PMCID: PMC8167110 DOI: 10.1038/s41389-021-00334-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/03/2021] [Accepted: 05/14/2021] [Indexed: 12/28/2022] Open
Abstract
Matrix metalloproteinases (MMPs) modify bioactive factors via selective processing or degradation resulting in tumour-promoting or tumour-suppressive effects, such as those by MMP8 in various cancers. We mapped the substrates of MMP8 to elucidate its previously shown tumour-protective role in oral tongue squamous cell carcinoma (OTSCC). MMP8 overexpressing (+) HSC-3 cells, previously demonstrated to have reduced migration and invasion, showed enhanced cell-cell adhesion. By analysing the secretomes of MMP8 + and control cells with terminal amine isotopic labelling of substrates (TAILS) coupled with liquid chromatography and tandem mass spectrometry (LC-MS/MS), we identified 36 potential substrates of MMP8, including FXYD domain-containing ion transport regulator 5 (FXYD5). An anti-adhesive glycoprotein FXYD5 has been previously shown to predict poor survival in OTSCC. Cleavage of FXYD5 by MMP8 was confirmed using recombinant proteins. Furthermore, we detected a loss of FXYD5 levels on cell membrane of MMP8 + cells, which was rescued by inhibition of the proteolytic activity of MMP8. Silencing (si) FXYD5 increased the cell-cell adhesion of control but not that of MMP8 + cells. siFXYD5 diminished the viability and motility of HSC-3 cells independent of MMP8 and similar effects were seen in another tongue cancer cell line, SCC-25. FXYD5 is a novel substrate of MMP8 and reducing FXYD5 levels either with siRNA or cleavage by MMP8 increases cell adhesion leading to reduced motility. FXYD5 being a known prognostic factor in OTSCC, our findings strengthen its potential as a therapeutic target.
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Affiliation(s)
- K Juurikka
- Cancer and Translational Medicine Research Unit, Faculty of Medicine, University of Oulu, Oulu, Finland.,Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - A Dufour
- Department of Physiology & Pharmacology, University of Calgary, Calgary, Canada.,Department of Oral Biological and Medical Sciences, Faculty of Dentistry, Centre for Blood Research, and Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada
| | - K Pehkonen
- Cancer and Translational Medicine Research Unit, Faculty of Medicine, University of Oulu, Oulu, Finland.,Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - B Mainoli
- Department of Physiology & Pharmacology, University of Calgary, Calgary, Canada
| | - P Campioni Rodrigues
- Cancer and Translational Medicine Research Unit, Faculty of Medicine, University of Oulu, Oulu, Finland.,Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - N Solis
- Department of Oral Biological and Medical Sciences, Faculty of Dentistry, Centre for Blood Research, and Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada
| | - T Klein
- Department of Oral Biological and Medical Sciences, Faculty of Dentistry, Centre for Blood Research, and Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada
| | - P Nyberg
- Cancer and Translational Medicine Research Unit, Faculty of Medicine, University of Oulu, Oulu, Finland.,Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland.,Biobank Borealis of Northern Finland, Oulu University Hospital, Oulu, Finland
| | - C M Overall
- Department of Oral Biological and Medical Sciences, Faculty of Dentistry, Centre for Blood Research, and Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada
| | - T Salo
- Cancer and Translational Medicine Research Unit, Faculty of Medicine, University of Oulu, Oulu, Finland.,Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland.,Department of Oral and Maxillofacial Diseases, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Helsinki University Hospital, Helsinki, Finland.,Translational Immunology Research Program (TRIMM), University of Helsinki, Helsinki, Finland
| | - P Åström
- Cancer and Translational Medicine Research Unit, Faculty of Medicine, University of Oulu, Oulu, Finland. .,Department of Oral Biological and Medical Sciences, Faculty of Dentistry, Centre for Blood Research, and Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada. .,Research Unit of Biomedicine, Faculty of Medicine, University of Oulu, Oulu, Finland.
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Weng L, Laboureur L, Wang Q, Guo L, Xu P, Gottlieb L, Lynch DR, Mesaros C, Blair IA. Extra-mitochondrial mouse frataxin and its implications for mouse models of Friedreich's ataxia. Sci Rep 2020; 10:15788. [PMID: 32978498 PMCID: PMC7519113 DOI: 10.1038/s41598-020-72884-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 08/28/2020] [Indexed: 01/04/2023] Open
Abstract
Mature frataxin is essential for the assembly of iron-sulfur cluster proteins including a number of mitochondrial enzymes. Reduced levels of mature frataxin (81-20) in human subjects caused by the genetic disease Friedreich's ataxia results in decreased mitochondrial function, neurodegeneration, and cardiomyopathy. Numerous studies of mitochondrial dysfunction have been conducted using mouse models of frataxin deficiency. However, mouse frataxin that is reduced in these models, is assumed to be mature frataxin (78-207) by analogy with human mature frataxin (81-210). Using immunoaffinity purification coupled with liquid chromatography-high resolution tandem mass spectrometry, we have discovered that mature frataxin in mouse heart (77%), brain (86%), and liver (47%) is predominantly a 129-amino acid truncated mature frataxin (79-207) in which the N-terminal lysine residue has been lost. Mature mouse frataxin (78-207) only contributes 7-15% to the total frataxin protein present in mouse tissues. We have also found that truncated mature frataxin (79-207) is present primarily in the cytosol of mouse liver; whereas, frataxin (78-207) is primarily present in the mitochondria. These findings, which provide support for the role of extra-mitochondrial frataxin in the etiology of Friedreich's ataxia, also have important implications for studies of mitochondrial dysfunction conducted in mouse models of frataxin deficiency.
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Affiliation(s)
- Liwei Weng
- Penn Medicine/CHOP Center of Excellence in Friedreich's Ataxia, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Center of Excellence in Environmental Toxicology, Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Laurent Laboureur
- Penn Medicine/CHOP Center of Excellence in Friedreich's Ataxia, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Center of Excellence in Environmental Toxicology, Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Qingqing Wang
- Penn Medicine/CHOP Center of Excellence in Friedreich's Ataxia, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Center of Excellence in Environmental Toxicology, Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Lili Guo
- Penn Medicine/CHOP Center of Excellence in Friedreich's Ataxia, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Center of Excellence in Environmental Toxicology, Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Peining Xu
- Penn Medicine/CHOP Center of Excellence in Friedreich's Ataxia, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Center of Excellence in Environmental Toxicology, Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Leah Gottlieb
- Penn Medicine/CHOP Center of Excellence in Friedreich's Ataxia, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Center of Excellence in Environmental Toxicology, Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - David R Lynch
- Penn Medicine/CHOP Center of Excellence in Friedreich's Ataxia, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Departments of Pediatrics and Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Clementina Mesaros
- Penn Medicine/CHOP Center of Excellence in Friedreich's Ataxia, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Center of Excellence in Environmental Toxicology, Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Ian A Blair
- Penn Medicine/CHOP Center of Excellence in Friedreich's Ataxia, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Center of Excellence in Environmental Toxicology, Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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