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Demeuse J, Massonnet P, Schoumacher M, Grifnée E, Huyghebaert L, Dubrowski T, Peeters S, Le Goff C, Cavalier E. Innovative workflow for the identification of cathepsin K cleavage sites in type I collagen. J Chromatogr B Analyt Technol Biomed Life Sci 2023; 1228:123864. [PMID: 37634391 DOI: 10.1016/j.jchromb.2023.123864] [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: 04/25/2023] [Revised: 08/09/2023] [Accepted: 08/19/2023] [Indexed: 08/29/2023]
Abstract
Since the late 1990s, cathepsin K cleavage sites in type I collagen have been extensively studied due to its ability to release bone resorption biomarkers such as CTX and NTX. However, gel-based methods and N-sequencing used in these studies lack sensitivity, especially for small to medium peptides. In this work, we propose a degradomics mass spectrometry-based workflow that combines protein digestion, Nano-LC-UDMSE, and several software tools to identify cathepsin K cleavage sites. This workflow not only identified previously known cleavage sites, but also discovered new ones. Multiple cleavage hotspots were found and described in type I α1 and type I α2 collagen, many of which coincided with pyridinoline crosslinks, known to stabilize the triple helix. Our results allowed us to establish a chronology of digestion and conclude that cathepsin K preferentially cleaves the extremities of type I collagen before the helical part. We also found that cathepsin K preferentially cleaves amino acid residues with long and hydrophobic lateral chains at the beginning of digestion, whereas no preferred amino acid residues were identified later in the digestion. In conclusion, our workflow successfully identified new cleavage sites and can be easily applied to other proteins or proteases.
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Affiliation(s)
- Justine Demeuse
- Department of Clinical Chemistry, CIRM, University of Liège, 4000 Liège, Belgium.
| | - Philippe Massonnet
- Department of Clinical Chemistry, University Hospital of Liège, 4000 Liège, Belgium
| | - Matthieu Schoumacher
- Department of Clinical Chemistry, CIRM, University of Liège, 4000 Liège, Belgium
| | - Elodie Grifnée
- Department of Clinical Chemistry, University Hospital of Liège, 4000 Liège, Belgium
| | - Loreen Huyghebaert
- Department of Clinical Chemistry, University Hospital of Liège, 4000 Liège, Belgium
| | - Thomas Dubrowski
- Department of Clinical Chemistry, University Hospital of Liège, 4000 Liège, Belgium
| | - Stéphanie Peeters
- Department of Clinical Chemistry, University Hospital of Liège, 4000 Liège, Belgium
| | - Caroline Le Goff
- Department of Clinical Chemistry, CIRM, University of Liège, 4000 Liège, Belgium; Department of Clinical Chemistry, University Hospital of Liège, 4000 Liège, Belgium
| | - Etienne Cavalier
- Department of Clinical Chemistry, CIRM, University of Liège, 4000 Liège, Belgium; Department of Clinical Chemistry, University Hospital of Liège, 4000 Liège, Belgium
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Yang Y, Li W, Liu C, Liu J, Yang L, Yue W, Yang L, Xue R, Zhang K, Zhang H, Chang N, Li L. Single-cell RNA seq identifies Plg-R KT-PLG as signals inducing phenotypic transformation of scar-associated macrophage in liver fibrosis. Biochim Biophys Acta Mol Basis Dis 2023; 1869:166754. [PMID: 37207518 DOI: 10.1016/j.bbadis.2023.166754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 05/05/2023] [Accepted: 05/09/2023] [Indexed: 05/21/2023]
Abstract
Hepatic macrophages play a central role in liver fibrosis. Scar-associated macrophages (SAMs), a recently identified subgroup of macrophages, play an important role in this process. However, the mechanism by which SAMs transform during liver fibrosis is still unclear. In this study, we aimed to characterize SAMs and elucidate the underlying mechanism of SAM transformation. Bile duct ligation (BDL) and carbon tetrachloride (CCl4) were used to induce mouse liver fibrosis. Non-parenchymal cells were isolated from normal/fibrotic livers and were analyzed using single cell RNA sequencing (scRNA-seq) or mass cytometry (CyTOF). The glucan-encapsulated siRNA particles (siRNA-GeRPs) was employed to perform macrophage selective gene knockdown. The results of scRNA-seq and CyTOF revealed that SAMs, which derived from bone marrow-derived macrophages (BMMs), accumulated in mouse fibrotic livers. Further analysis showed that SAMs highly expressed genes related to fibrosis, indicating the pro-fibrotic functions of SAMs. Moreover, plasminogen receptor Plg-RKT was highly expressed by SAMs, suggesting the role of Plg-RKT and plasminogen (PLG) in SAM transformation. In vitro, PLG-treated BMMs transformed into SAMs and expressed SAM functional genes. Knockdown of Plg-RKT blocked the effects of PLG. In vivo, selective knockdown of Plg-RKT in intrahepatic macrophages of BDL- and CCl4-treated mice reduced the number of SAMs and alleviated BDL- and CCl4-induced liver fibrosis, suggesting that Plg-RKT-PLG played an important role in liver fibrosis by mediating SAM transformation. Our findings reveal that SAMs are crucial participants in liver fibrosis. Inhibition of SAM transformation by blocking Plg-RKT might be a potential therapeutic target for liver fibrosis.
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Affiliation(s)
- Yuanru Yang
- Department of Cell Biology, Municipal Laboratory for Liver Protection and Regulation of Regeneration, Capital Medical University, Beijing 100069, China
| | - Weiyang Li
- Department of Cell Biology, Municipal Laboratory for Liver Protection and Regulation of Regeneration, Capital Medical University, Beijing 100069, China
| | - Chang Liu
- Department of Cell Biology, Municipal Laboratory for Liver Protection and Regulation of Regeneration, Capital Medical University, Beijing 100069, China
| | - Jing Liu
- Department of Cell Biology, Municipal Laboratory for Liver Protection and Regulation of Regeneration, Capital Medical University, Beijing 100069, China
| | - Lin Yang
- Department of Cell Biology, Municipal Laboratory for Liver Protection and Regulation of Regeneration, Capital Medical University, Beijing 100069, China
| | - Wenhui Yue
- Department of Cell Biology, Municipal Laboratory for Liver Protection and Regulation of Regeneration, Capital Medical University, Beijing 100069, China
| | - Le Yang
- Department of Cell Biology, Municipal Laboratory for Liver Protection and Regulation of Regeneration, Capital Medical University, Beijing 100069, China
| | - Renmin Xue
- Department of Cell Biology, Municipal Laboratory for Liver Protection and Regulation of Regeneration, Capital Medical University, Beijing 100069, China
| | - Kai Zhang
- Department of Cell Biology, Municipal Laboratory for Liver Protection and Regulation of Regeneration, Capital Medical University, Beijing 100069, China
| | - Hang Zhang
- Department of Cell Biology, Municipal Laboratory for Liver Protection and Regulation of Regeneration, Capital Medical University, Beijing 100069, China
| | - Na Chang
- Department of Cell Biology, Municipal Laboratory for Liver Protection and Regulation of Regeneration, Capital Medical University, Beijing 100069, China.
| | - Liying Li
- Department of Cell Biology, Municipal Laboratory for Liver Protection and Regulation of Regeneration, Capital Medical University, Beijing 100069, China.
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Elhendawy HA, Soliman S. Clinicopathological correlation of Cathepsin K expression in salivary gland carcinomas; relation to patients` outcome. Diagn Pathol 2023; 18:66. [PMID: 37198626 DOI: 10.1186/s13000-023-01353-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 05/07/2023] [Indexed: 05/19/2023] Open
Abstract
BACKGROUND Salivary gland carcinomas (SGCs) represent various groups of tumors that demonstrate marked diversity in their prognosis owing to different histology and clinical characteristics. One of the poor prognostic indicators is distant metastasis which is considered the major reason for death in SGC patients. Discovering new biomarkers is urgently required to aid in the detection of cancer onset and progression. Cathepsin K (CTSK), the lysosomal cysteine protease has a principal role in cancer invasion and progression through interaction with the tumor microenvironment, degradation of extracellular membrane proteins and destruction of the elastic lamina of blood vessels. In the English literature, little information was present about the role of CTSK in SGCs. The current study aimed to assess the immunohistochemical expression of CTSK in SGCs and correlate its expression to different clinicopathologic parameters. METHODS The retrospective study applied to 45 cases of SGCs categorized as high-grade (33 cases) and low-grade SGCs (12 cases) following the criteria of WHO classification (2017) of head and neck tumors. All patients` clinicopathological and follow-up records were retrieved. The following statistical tests were used to study the variance of CTSK expression in SGCs concerning different clinicopathological parameters; Pearson`s Chi-square test, unpaired two-tailed student t-test, One-way ANOVA, and Post Hoc tests. Disease-free survival (DFS) and Overall survival (OS) were calculated and displayed with the Kaplan-Meier strategy and analyzed with the log-rank test. Univariate and multivariate survival analyses were performed with Cox regression. A P-value lesser than 0.05 was considered statistically significant. RESULTS Strong CTSK expression was significantly related to high-grade SGCs (P = 0.000), large infiltrating carcinomas (P = 0.000), presence of nodal (P = 0.041) and distant metastasis (P = 0.009), advanced TNM clinical stage (P = 0.000), the incidence of recurrence (P = 0.009), and reduced DFS (P = 0.006). Distant metastasis was the independent predictor for DFS using Cox regression model. CONCLUSIONS CTSK has a great role in cancer progression by triggering many signaling pathways. Its level in cancerous tissue is considered an effective index for predicting the severity and prognosis of cancer. Therefore, we indicate its utility as a prognostic tool and therapeutic target for cancer treatment. TRIAL REGISTRATION Retrospectively registered.
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Affiliation(s)
- Heba Ahmed Elhendawy
- Oral Pathology Department, Faculty of Dentistry, Mansoura University, Mansoura, Egypt
| | - Samar Soliman
- Oral Pathology Department, Faculty of Dentistry, Mansoura University, Mansoura, Egypt.
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Višnić A, Čanadi Jurešić G, Domitrović R, Klarić M, Šepić TS, Barišić D. Proteins in urine - Possible biomarkers of endometriosis. J Reprod Immunol 2023; 157:103941. [PMID: 36948095 DOI: 10.1016/j.jri.2023.103941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 03/08/2023] [Accepted: 03/16/2023] [Indexed: 03/19/2023]
Abstract
In the pathogenesis of endometriosis, a number of pathological reactions occur. Proteins secreted in the urine are thought to interact with each other and stimulate the pathological processes in endometriosis. Identifying one or more proteins that are specific enough and could serve as biomarkers for endometriosis is both a challenge and a necessity that would facilitate diagnosis. The urine of patients treated in a tertiary university hospital between July 1, 2020 and June 30, 2021 was analyzed. The studied group consists of patients who were treated surgically for endometriosis and in whom the diagnosis was confirmed by pathohistological analysis. The control group consists of patients who were operated for functional ovarian cysts. Urinary proteins were analyzed by chromatography and mass spectrometry (LC-MS/MS). We identified 17 proteins in urine whose concentrations were statistically significantly different in the group with endometriosis (N = 16) compared with the control groups (N = 16). The detected proteins were classified into groups according to their function in invasion, migration and proliferation, proteolysis, immune system, cell adhesion and vascular system. For all mentioned proteins the difference in concentration is statistically significant p < 0.005. Proteins are secreted in the urine of patients with endometriosis that may be involved in the pathogenesis of the disease and are possible biomarkers for endometriosis.
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Affiliation(s)
- Alenka Višnić
- Clinical Hospital Center Rijeka, Clinic for Gynecology and Obstetrics, Rijeka, Croatia
| | - Gordana Čanadi Jurešić
- Department of Medical Chemistry, Biochemistry and Clinical Chemistry, Faculty of Medicine, University in Rijeka, Rijeka, Croatia.
| | - Robert Domitrović
- Department of Medical Chemistry, Biochemistry and Clinical Chemistry, Faculty of Medicine, University in Rijeka, Rijeka, Croatia
| | - Marko Klarić
- Clinical Hospital Center Rijeka, Clinic for Gynecology and Obstetrics, Rijeka, Croatia
| | - Tina Sušanj Šepić
- Clinical Hospital Center Rijeka, Clinic for Gynecology and Obstetrics, Rijeka, Croatia
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Mohindra R, Mohindra R, Agrawal DK, Thankam FG. Bioactive extracellular matrix fragments in tendon repair. Cell Tissue Res 2022; 390:131-140. [PMID: 36074173 DOI: 10.1007/s00441-022-03684-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 08/30/2022] [Indexed: 11/02/2022]
Abstract
Tendinopathy is a common tendon disorder that causes pain, loss of strength and function, and local inflammation mainly characterized by hypoxia, collagen degradation, and extracellular matrix (ECM) disorganization. Generally, ECM degradation and remodeling is tightly regulated; however, hyperactivation of matrix metalloproteases (MMPs) contributes to excessive collagenolysis under pathologic conditions resulting in tendon ECM degradation. This review article focuses on the production, function, and signaling of matrikines for tendon regeneration following injury with insights into the expression, tissue compliance, and cell proliferation exhibited by various matrikines. Furthermore, the regenerative properties suggest translational significance of matrikines to improve the outcomes post-injury by assisting with tendon healing.
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Affiliation(s)
- Ritika Mohindra
- Department of Translational Research, Western University of Health Sciences, 309 E. Second Street, Pomona, CA, 91766-1854, USA
| | - Rohit Mohindra
- Department of Translational Research, Western University of Health Sciences, 309 E. Second Street, Pomona, CA, 91766-1854, USA
| | - Devendra K Agrawal
- Department of Translational Research, Western University of Health Sciences, 309 E. Second Street, Pomona, CA, 91766-1854, USA
| | - Finosh G Thankam
- Department of Translational Research, Western University of Health Sciences, 309 E. Second Street, Pomona, CA, 91766-1854, USA.
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Cathepsin K: A Versatile Potential Biomarker and Therapeutic Target for Various Cancers. Curr Oncol 2022; 29:5963-5987. [PMID: 36005209 PMCID: PMC9406569 DOI: 10.3390/curroncol29080471] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 08/15/2022] [Accepted: 08/21/2022] [Indexed: 12/11/2022] Open
Abstract
Cancer, a common malignant disease, is one of the predominant causes of diseases that lead to death. Additionally, cancer is often detected in advanced stages and cannot be radically cured. Consequently, there is an urgent need for reliable and easily detectable markers to identify and monitor cancer onset and progression as early as possible. Our aim was to systematically review the relevant roles of cathepsin K (CTSK) in various possible cancers in existing studies. CTSK, a well-known key enzyme in the bone resorption process and most studied for its roles in the effective degradation of the bone extracellular matrix, is expressed in various organs. Nowadays, CTSK has been involved in various cancers such as prostate cancer, breast cancer, bone cancer, renal carcinoma, lung cancer and other cancers. In addition, CTSK can promote tumor cells proliferation, invasion and migration, and its mechanism may be related to RANK/RANKL, TGF-β, mTOR and the Wnt/β-catenin signaling pathway. Clinically, some progress has been made with the use of cathepsin K inhibitors in the treatment of certain cancers. This paper reviewed our current understanding of the possible roles of CTSK in various cancers and discussed its potential as a biomarker and/or novel molecular target for various cancers.
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Peptides and Peptidomimetics as Inhibitors of Enzymes Involved in Fibrillar Collagen Degradation. MATERIALS 2021; 14:ma14123217. [PMID: 34200889 PMCID: PMC8230458 DOI: 10.3390/ma14123217] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 05/28/2021] [Accepted: 06/07/2021] [Indexed: 12/20/2022]
Abstract
Collagen fibres degradation is a complex process involving a variety of enzymes. Fibrillar collagens, namely type I, II, and III, are the most widely spread collagens in human body, e.g., they are responsible for tissue fibrillar structure and skin elasticity. Nevertheless, the hyperactivity of fibrotic process and collagen accumulation results with joints, bone, heart, lungs, kidneys or liver fibroses. Per contra, dysfunctional collagen turnover and its increased degradation leads to wound healing disruption, skin photoaging, and loss of firmness and elasticity. In this review we described the main enzymes participating in collagen degradation pathway, paying particular attention to enzymes degrading fibrillar collagen. Therefore, collagenases (MMP-1, -8, and -13), elastases, and cathepsins, together with their peptide and peptidomimetic inhibitors, are reviewed. This information, related to the design and synthesis of new inhibitors based on peptide structure, can be relevant for future research in the fields of chemistry, biology, medicine, and cosmeceuticals.
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Thankam FG, Agrawal DK. Hypoxia-driven secretion of extracellular matrix proteins in the exosomes reflects the asymptomatic pathology of rotator cuff tendinopathies. Can J Physiol Pharmacol 2020; 99:224-230. [PMID: 32799660 DOI: 10.1139/cjpp-2020-0314] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The major hallmark of rotator cuff tendinopathies (RCT) is the disorganization of the tendon extracellular matrix (ECM), which is due to a decrease in the ratio of collagen I to collagen III. In addition, the pathology of the tendon matrisome remains asymptomatic, and hypoxia has been identified to be the priming signal to initiate the molecular pathology of RCT. Also, the secretome content of hypoxia-challenged tendon cells (tenocytes) reflects the pathological status of RCT. With this background, the present study was designed to establish the expression status and molecular crosstalk of the ECM component proteins contained in the exosomes of the hypoxia-challenged swine tenocytes. The mass spectrometry analysis revealed the upregulation of COL1A2, P4HA1, PRDX2, P3H1, COL6A1, PPIB, LCN1, and COL3A1 and the downregulation of COLA12, PDIA4, COLG, FN1, CTSK, and TNC in the exosomes of hypoxic tenocytes. These proteins interact with diverse proteins and operate multiple pathways associated with ECM homeostasis and repair as determined by NetworkAnalyst. The functional analysis of these proteins reflects the pathology of tendon ECM, which is correlated with the asymptomatic phase of RCT. Understanding the signaling mediated by these proteins would reveal the underlying molecular pathology and offers translational significance in the diagnosis and management of RCT.
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Affiliation(s)
- Finosh G Thankam
- Department of Translational Research, Western University of Health Sciences, Pomona, CA 91766, USA.,Department of Translational Research, Western University of Health Sciences, Pomona, CA 91766, USA
| | - Devendra K Agrawal
- Department of Translational Research, Western University of Health Sciences, Pomona, CA 91766, USA.,Department of Translational Research, Western University of Health Sciences, Pomona, CA 91766, USA
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Reassessing enzyme kinetics: Considering protease-as-substrate interactions in proteolytic networks. Proc Natl Acad Sci U S A 2020; 117:3307-3318. [PMID: 31980525 DOI: 10.1073/pnas.1912207117] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Enzymes are catalysts in biochemical reactions that, by definition, increase rates of reactions without being altered or destroyed. However, when that enzyme is a protease, a subclass of enzymes that hydrolyze other proteins, and that protease is in a multiprotease system, protease-as-substrate dynamics must be included, challenging assumptions of enzyme inertness, shifting kinetic predictions of that system. Protease-on-protease inactivating hydrolysis can alter predicted protease concentrations used to determine pharmaceutical dosing strategies. Cysteine cathepsins are proteases capable of cathepsin cannibalism, where one cathepsin hydrolyzes another with substrate present, and misunderstanding of these dynamics may cause miscalculations of multiple proteases working in one proteolytic network of interactions occurring in a defined compartment. Once rates for individual protease-on-protease binding and catalysis are determined, proteolytic network dynamics can be explored using computational models of cooperative/competitive degradation by multiple proteases in one system, while simultaneously incorporating substrate cleavage. During parameter optimization, it was revealed that additional distraction reactions, where inactivated proteases become competitive inhibitors to remaining, active proteases, occurred, introducing another network reaction node. Taken together, improved predictions of substrate degradation in a multiple protease network were achieved after including reaction terms of autodigestion, inactivation, cannibalism, and distraction, altering kinetic considerations from other enzymatic systems, since enzyme can be lost to proteolytic degradation. We compiled and encoded these dynamics into an online platform (https://plattlab.shinyapps.io/catKLS/) for individual users to test hypotheses of specific perturbations to multiple cathepsins, substrates, and inhibitors, and predict shifts in proteolytic network reactions and system dynamics.
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