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Cook L, Gharzia FG, Bartsch JW, Yildiz D. A jack of all trades - ADAM8 as a signaling hub in inflammation and cancer. FEBS J 2023. [PMID: 38097912 DOI: 10.1111/febs.17034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/23/2023] [Accepted: 12/12/2023] [Indexed: 12/23/2023]
Abstract
As a member of the family of A Disintegrin And Metalloproteinases (ADAM) ADAM8 is preferentially expressed in lymphatic organs, immune cells, and tumor cells. The substrate spectrum for ADAM8 proteolytic activity is not exclusive but is related to effectors of inflammation and signaling in the tumor microenvironment. In addition, complexes of ADAM8 with extracellular binding partners such as integrin β-1 cause an extensive intracellular signaling in tumor cells, thereby activating kinase pathways with STAT3, ERK1/2, and Akt signaling, which causes increased cell survival and enhanced motility. The cytoplasmic domain of ADAM8 harbors five SRC homology-3 (SH3) domains that can potentially interact with several proteins involved in actin dynamics and cell motility, including Myosin 1F (MYO1F), which is essential for neutrophil motility. The concept of ADAM8 thus involves immune cell recruitment, in most cases leading to an enhancement of inflammatory (asthma, COPD) and tumor (including pancreatic and breast cancers) pathologies. In this review, we report on available studies that qualify ADAM8 as a therapeutic target in different pathologies. As a signaling hub, ADAM8 controls extracellular, intracellular, and intercellular communication, the latter one mainly mediated by the release of extracellular vesicles with ADAM8 as cargo. Here, we will dissect the contribution of different domains to these distinct ways of communication in several pathologies. We conclude that therapeutic targeting attempts for ADAM8 should consider blocking more than a single domain and that this requires a thorough evaluation of potent molecules targeting ADAM8 in an in vivo setting.
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Affiliation(s)
- Lena Cook
- Department of Neurosurgery, Philipps University Marburg, Germany
| | - Federico Guillermo Gharzia
- Experimental and Clinical Pharmacology and Toxicology Center for Molecular Signaling (PZMS), Saarland University, Homburg, Germany
| | - Jörg W Bartsch
- Department of Neurosurgery, Philipps University Marburg, Germany
| | - Daniela Yildiz
- Experimental and Clinical Pharmacology and Toxicology Center for Molecular Signaling (PZMS), Saarland University, Homburg, Germany
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2
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Holt BA, Lim HS, Sivakumar A, Phuengkham H, Su M, Tuttle M, Xu Y, Liakakos H, Qiu P, Kwong GA. Embracing enzyme promiscuity with activity-based compressed biosensing. CELL REPORTS METHODS 2023; 3:100372. [PMID: 36814844 PMCID: PMC9939361 DOI: 10.1016/j.crmeth.2022.100372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 10/11/2022] [Accepted: 12/06/2022] [Indexed: 12/31/2022]
Abstract
The development of protease-activatable drugs and diagnostics requires identifying substrates specific to individual proteases. However, this process becomes increasingly difficult as the number of target proteases increases because most substrates are promiscuously cleaved by multiple proteases. We introduce a method-substrate libraries for compressed sensing of enzymes (SLICE)-for selecting libraries of promiscuous substrates that classify protease mixtures (1) without deconvolution of compressed signals and (2) without highly specific substrates. SLICE ranks substrate libraries using a compression score (C), which quantifies substrate orthogonality and protease coverage. This metric is predictive of classification accuracy across 140 in silico (Pearson r = 0.71) and 55 in vitro libraries (r = 0.55). Using SLICE, we select a two-substrate library to classify 28 samples containing 11 enzymes in plasma (area under the receiver operating characteristic curve [AUROC] = 0.93). We envision that SLICE will enable the selection of libraries that capture information from hundreds of enzymes using fewer substrates for applications like activity-based sensors for imaging and diagnostics.
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Affiliation(s)
- Brandon Alexander Holt
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, GA 30332, USA
| | - Hong Seo Lim
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, GA 30332, USA
| | - Anirudh Sivakumar
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, GA 30332, USA
| | - Hathaichanok Phuengkham
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, GA 30332, USA
| | - Melanie Su
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, GA 30332, USA
| | - McKenzie Tuttle
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, GA 30332, USA
| | - Yilin Xu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, GA 30332, USA
| | - Haley Liakakos
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, GA 30332, USA
| | - Peng Qiu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, GA 30332, USA
| | - Gabriel A. Kwong
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, GA 30332, USA
- Parker H. Petit Institute of Bioengineering and Bioscience, Atlanta, GA 30332, USA
- Institute for Electronics and Nanotechnology, Georgia Tech, Atlanta, GA 30332, USA
- Integrated Cancer Research Center, Georgia Tech, Atlanta, GA 30332, USA
- Georgia ImmunoEngineering Consortium, Georgia Tech and Emory University, Atlanta, GA 30332, USA
- Emory School of Medicine, Atlanta, GA 30332, USA
- Emory Winship Cancer Institute, Atlanta, GA 30322, USA
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3
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Austin MJ, Schunk H, Watkins C, Ling N, Chauvin J, Morton L, Rosales AM. Fluorescent Peptomer Substrates for Differential Degradation by Metalloproteases. Biomacromolecules 2022; 23:4909-4923. [PMID: 36269900 DOI: 10.1021/acs.biomac.2c01077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Proteases, especially MMPs, are attractive biomarkers given their central role in both physiological and pathological processes. Distinguishing MMP activity with degradable substrates, however, is a difficult task due to overlapping substrate specificity profiles. Here, we developed a system of peptomers (peptide-peptoid hybrids) to probe the impact of non-natural residues on MMP specificity for an MMP peptide consensus sequence. Peptoids are non-natural, N-substituted glycines with a large side-chain diversity. Given the presence of a hallmark proline residue in the P3 position of MMP consensus sequences, we hypothesized that peptoids may offer N-substituted alternatives to generate differential interactions with MMPs. To investigate this hypothesis, peptomer substrates were exposed to five different MMPs, as well as bacterial collagenase, and monitored by fluorescence resonance energy transfer and liquid chromatography-mass spectrometry to determine the rate of cleavage and the composition of degraded fragments, respectively. We found that peptoid residues are well tolerated in the P3 and P3' substrate sites and that the identity of the peptoid in these sites displays a moderate influence on the rate of cleavage. However, peptoid residues were even better tolerated in the P1 substrate site where activity was more strongly correlated with side-chain identity than side-chain position. All MMPs explored demonstrated similar trends in specificity for the peptomers but exhibited different degrees of variability in proteolytic rate. These kinetic profiles served as "fingerprints" for the proteases and yielded separation by multivariate data analysis. To further demonstrate the practical application of this tunability in degradation kinetics, peptomer substrates were tethered into hydrogels and released over distinct timescales. Overall, this work represents a significant step toward the design of probes that maximize differential MMP behavior and presents design rules to tune degradation kinetics with peptoid substitutions, which has promising implications for diagnostic and prognostic applications using array-based sensors.
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Affiliation(s)
- Mariah J Austin
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas78712, United States
| | - Hattie Schunk
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas78712, United States.,Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas78712, United States
| | - Carolyn Watkins
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas78712, United States
| | - Natalie Ling
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas78712, United States
| | - Jeremy Chauvin
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas78712, United States
| | - Logan Morton
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas78712, United States
| | - Adrianne M Rosales
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas78712, United States
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4
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Soleimany AP, Martin-Alonso C, Anahtar M, Wang CS, Bhatia SN. Protease Activity Analysis: A Toolkit for Analyzing Enzyme Activity Data. ACS OMEGA 2022; 7:24292-24301. [PMID: 35874224 PMCID: PMC9301967 DOI: 10.1021/acsomega.2c01559] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Analyzing the activity of proteases and their substrates is critical to defining the biological functions of these enzymes and to designing new diagnostics and therapeutics that target protease dysregulation in disease. While a wide range of databases and algorithms have been created to better predict protease cleavage sites, there is a dearth of computational tools to automate analysis of in vitro and in vivo protease assays. This necessitates individual researchers to develop their own analytical pipelines, resulting in a lack of standardization across the field. To facilitate protease research, here we present Protease Activity Analysis (PAA), a toolkit for the preprocessing, visualization, machine learning analysis, and querying of protease activity data sets. PAA leverages a Python-based object-oriented implementation that provides a modular framework for streamlined analysis across three major components. First, PAA provides a facile framework to query data sets of synthetic peptide substrates and their cleavage susceptibilities across a diverse set of proteases. To complement the database functionality, PAA also includes tools for the automated analysis and visualization of user-input enzyme-substrate activity measurements generated through in vitro screens against synthetic peptide substrates. Finally, PAA supports a set of modular machine learning functions to analyze in vivo protease activity signatures that are generated by activity-based sensors. Overall, PAA offers the protease community a breadth of computational tools to streamline research, taking a step toward standardizing data analysis across the field and in chemical biology and biochemistry at large.
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Affiliation(s)
- Ava P. Soleimany
- Harvard-MIT
Division of Health Sciences and Technology, MIT, Cambridge, Massachusetts 02139, United States
- Program
in Biophysics, Harvard University, Boston, Massachusetts 02115, United States
- Microsoft
Research New England, Cambridge, Massachusetts 02142, United States
| | - Carmen Martin-Alonso
- Harvard-MIT
Division of Health Sciences and Technology, MIT, Cambridge, Massachusetts 02139, United States
| | - Melodi Anahtar
- Harvard-MIT
Division of Health Sciences and Technology, MIT, Cambridge, Massachusetts 02139, United States
| | - Cathy S. Wang
- Department
of Biological Engineering, MIT, Cambridge, Massachusetts 02139, United States
| | - Sangeeta N. Bhatia
- Harvard-MIT
Division of Health Sciences and Technology, MIT, Cambridge, Massachusetts 02139, United States
- Department
of Electrical Engineering and Computer Science, MIT, Cambridge, Massachusetts 02139, United States
- Howard Hughes
Medical Institute, Cambridge, Massachusetts 02139, United States
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5
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Mac QD, Sivakumar A, Phuengkham H, Xu C, Bowen JR, Su FY, Stentz SZ, Sim H, Harris AM, Li TT, Qiu P, Kwong GA. Urinary detection of early responses to checkpoint blockade and of resistance to it via protease-cleaved antibody-conjugated sensors. Nat Biomed Eng 2022; 6:310-324. [PMID: 35241815 DOI: 10.1038/s41551-022-00852-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 01/28/2022] [Indexed: 12/15/2022]
Abstract
Immune checkpoint blockade (ICB) therapy does not benefit the majority of treated patients, and those who respond to the therapy can become resistant to it. Here we report the design and performance of systemically administered protease activity sensors conjugated to anti-programmed cell death protein 1 (αPD1) antibodies for the monitoring of antitumour responses to ICB therapy. The sensors consist of a library of mass-barcoded protease substrates that, when cleaved by tumour proteases and immune proteases, are released into urine, where they can be detected by mass spectrometry. By using syngeneic mouse models of colorectal cancer, we show that random forest classifiers trained on mass spectrometry signatures from a library of αPD1-conjugated mass-barcoded activity sensors for differentially expressed tumour proteases and immune proteases can be used to detect early antitumour responses and discriminate resistance to ICB therapy driven by loss-of-function mutations in either the B2m or Jak1 genes. Biomarkers of protease activity may facilitate the assessment of early responses to ICB therapy and the classification of refractory tumours based on resistance mechanisms.
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Affiliation(s)
- Quoc D Mac
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, GA, USA
| | - Anirudh Sivakumar
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, GA, USA
| | - Hathaichanok Phuengkham
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, GA, USA
| | - Congmin Xu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, GA, USA
| | - James R Bowen
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, GA, USA
| | - Fang-Yi Su
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, GA, USA
| | - Samuel Z Stentz
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, GA, USA
| | - Hyoungjun Sim
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, GA, USA
| | - Adrian M Harris
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, GA, USA
| | - Tonia T Li
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, GA, USA
| | - Peng Qiu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, GA, USA.,Parker H. Petit Institute for Bioengineering and Bioscience, Atlanta, GA, USA.,The Georgia Immunoengineering Consortium, Emory University and Georgia Tech, Atlanta, GA, USA.,Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - Gabriel A Kwong
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, GA, USA. .,Parker H. Petit Institute for Bioengineering and Bioscience, Atlanta, GA, USA. .,The Georgia Immunoengineering Consortium, Emory University and Georgia Tech, Atlanta, GA, USA. .,Winship Cancer Institute, Emory University, Atlanta, GA, USA. .,Institute for Electronics and Nanotechnology, Georgia Tech, Atlanta, GA, USA. .,Integrated Cancer Research Center, Georgia Tech, Atlanta, GA, USA.
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6
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Cook L, Sengelmann M, Winkler B, Nagl C, Koch S, Schlomann U, Slater EP, Miller MA, von Strandmann EP, Dörsam B, Preußer C, Bartsch JW. ADAM8-Dependent Extracellular Signaling in the Tumor Microenvironment Involves Regulated Release of Lipocalin 2 and MMP-9. Int J Mol Sci 2022; 23:ijms23041976. [PMID: 35216088 PMCID: PMC8875419 DOI: 10.3390/ijms23041976] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/03/2022] [Accepted: 02/08/2022] [Indexed: 12/11/2022] Open
Abstract
The metalloprotease-disintegrin ADAM8 is critically involved in the progression of pancreatic cancer. Under malignant conditions, ADAM8 is highly expressed and could play an important role in cell–cell communication as expression has been observed in tumor and immune cells of the tumor microenvironment (TME) such as macrophages. To analyze the potential role of ADAM8 in the TME, ADAM8 knockout PDAC tumor cells were generated, and their release of extracellular vesicles (EVs) was analyzed. In EVs, ADAM8 is present as an active protease and associated with lipocalin 2 (LCN2) and matrix metalloprotease 9 (MMP-9) in an ADAM8-dependent manner, as ADAM8 KO cells show a lower abundance of LCN2 and MMP-9. Sorting of ADAM8 occurs independent of TSG101, even though ADAM8 contains the recognition motif PTAP for the ESCRTI protein TSG101 within the cytoplasmic domain (CD). When tumor cells were co-cultured with macrophages (THP-1 cells), expression of LCN2 and MMP-9 in ADAM8 KO cells was induced, suggesting that macrophage signaling can overcome ADAM8-dependent intracellular signaling in PDAC cells. In co-culture with macrophages, regulation of MMP-9 is independent of the M1/M2 polarization state, whereas LCN2 expression is preferentially affected by M1-like macrophages. From these data, we conclude that ADAM8 has a systemic effect in the tumor microenvironment, and its expression in distinct cell types has to be considered for ADAM8 targeting in tumors.
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Affiliation(s)
- Lena Cook
- Department of Neurosurgery, Philipps University Marburg, Baldingerstr, 35033 Marburg, Germany; (L.C.); (M.S.); (B.W.); (C.N.); (S.K.); (U.S.)
| | - Marie Sengelmann
- Department of Neurosurgery, Philipps University Marburg, Baldingerstr, 35033 Marburg, Germany; (L.C.); (M.S.); (B.W.); (C.N.); (S.K.); (U.S.)
| | - Birte Winkler
- Department of Neurosurgery, Philipps University Marburg, Baldingerstr, 35033 Marburg, Germany; (L.C.); (M.S.); (B.W.); (C.N.); (S.K.); (U.S.)
| | - Constanze Nagl
- Department of Neurosurgery, Philipps University Marburg, Baldingerstr, 35033 Marburg, Germany; (L.C.); (M.S.); (B.W.); (C.N.); (S.K.); (U.S.)
| | - Sarah Koch
- Department of Neurosurgery, Philipps University Marburg, Baldingerstr, 35033 Marburg, Germany; (L.C.); (M.S.); (B.W.); (C.N.); (S.K.); (U.S.)
| | - Uwe Schlomann
- Department of Neurosurgery, Philipps University Marburg, Baldingerstr, 35033 Marburg, Germany; (L.C.); (M.S.); (B.W.); (C.N.); (S.K.); (U.S.)
- Department of Visceral Surgery, Philipps University Marburg, Baldingerstr, 35033 Marburg, Germany;
| | - Emily P. Slater
- Department of Visceral Surgery, Philipps University Marburg, Baldingerstr, 35033 Marburg, Germany;
| | - Miles A. Miller
- Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA;
| | - Elke Pogge von Strandmann
- Department of Medicine, Institute for Tumor Immunology, Philipps University Marburg, 35043 Marburg, Germany; (E.P.v.S.); (B.D.); (C.P.)
| | - Bastian Dörsam
- Department of Medicine, Institute for Tumor Immunology, Philipps University Marburg, 35043 Marburg, Germany; (E.P.v.S.); (B.D.); (C.P.)
| | - Christian Preußer
- Department of Medicine, Institute for Tumor Immunology, Philipps University Marburg, 35043 Marburg, Germany; (E.P.v.S.); (B.D.); (C.P.)
| | - Jörg W. Bartsch
- Department of Neurosurgery, Philipps University Marburg, Baldingerstr, 35033 Marburg, Germany; (L.C.); (M.S.); (B.W.); (C.N.); (S.K.); (U.S.)
- Correspondence: ; Tel.: +49-6421-58-61173
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7
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Conrad C, Yildiz D, Cleary SJ, Margraf A, Cook L, Schlomann U, Panaretou B, Bowser JL, Karmouty-Quintana H, Li J, Berg NK, Martin SC, Aljohmani A, Moussavi-Harami SF, Wang KM, Tian JJ, Magnen M, Valet C, Qiu L, Singer JP, Eltzschig HK, Bertrams W, Herold S, Suttorp N, Schmeck B, Ball ZT, Zarbock A, Looney MR, Bartsch JW. ADAM8 signaling drives neutrophil migration and ARDS severity. JCI Insight 2022; 7:e149870. [PMID: 35132956 PMCID: PMC8855804 DOI: 10.1172/jci.insight.149870] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 12/21/2021] [Indexed: 01/27/2023] Open
Abstract
Acute respiratory distress syndrome (ARDS) results in catastrophic lung failure and has an urgent, unmet need for improved early recognition and therapeutic development. Neutrophil influx is a hallmark of ARDS and is associated with the release of tissue-destructive immune effectors, such as matrix metalloproteinases (MMPs) and membrane-anchored metalloproteinase disintegrins (ADAMs). Here, we observed using intravital microscopy that Adam8-/- mice had impaired neutrophil transmigration. In mouse pneumonia models, both genetic deletion and pharmacologic inhibition of ADAM8 attenuated neutrophil infiltration and lung injury while improving bacterial containment. Unexpectedly, the alterations of neutrophil function were not attributable to impaired proteolysis but resulted from reduced intracellular interactions of ADAM8 with the actin-based motor molecule Myosin1f that suppressed neutrophil motility. In 2 ARDS cohorts, we analyzed lung fluid proteolytic signatures and identified that ADAM8 activity was positively correlated with disease severity. We propose that in acute inflammatory lung diseases such as pneumonia and ARDS, ADAM8 inhibition might allow fine-tuning of neutrophil responses for therapeutic gain.
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Affiliation(s)
- Catharina Conrad
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, School of Medicine, University of California, San Francisco, San Francisco, California, USA
- Department of Anesthesiology, Intensive Care and Pain Medicine, University Hospital Münster, Münster, Germany
| | - Daniela Yildiz
- Institute of Experimental and Clinical Pharmacology and Toxicology, PZMS, ZHMB, Saarland University, Homburg, Germany
| | - Simon J. Cleary
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, School of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Andreas Margraf
- Department of Anesthesiology, Intensive Care and Pain Medicine, University Hospital Münster, Münster, Germany
| | - Lena Cook
- Department of Neurosurgery/Lab, Faculty of Medicine, Philipps-University, Marburg, Germany
| | - Uwe Schlomann
- Department of Neurosurgery/Lab, Faculty of Medicine, Philipps-University, Marburg, Germany
| | - Barry Panaretou
- School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences & Medicine, King’s College London, London, United Kingdom
| | - Jessica L. Bowser
- Department of Pathology & Laboratory Medicine, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | | | - Jiwen Li
- Department of Anesthesiology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Nathaniel K. Berg
- Department of Anesthesiology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | | | - Ahmad Aljohmani
- Institute of Experimental and Clinical Pharmacology and Toxicology, PZMS, ZHMB, Saarland University, Homburg, Germany
| | - S. Farshid Moussavi-Harami
- Department of Pediatrics, Division of Pediatric Critical Care, University of California, San Francisco, San Francisco, California, USA
| | - Kristin M. Wang
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, School of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Jennifer J. Tian
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, School of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Mélia Magnen
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, School of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Colin Valet
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, School of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Longhui Qiu
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, School of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Jonathan P. Singer
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, School of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Holger K. Eltzschig
- Department of Anesthesiology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | | | - Wilhelm Bertrams
- Institute for Lung Research (iLung), Philipps-University, Marburg, Germany
| | - Susanne Herold
- Department of Internal Medicine II, University Medical Center Giessen and Marburg, Giessen, Germany
- Deutsches Zentrum für Lungenforschung (DZL), Giessen, Germany
| | - Norbert Suttorp
- Department of Internal Medicine/Infectious Diseases and Respiratory Medicine, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Bernd Schmeck
- Deutsches Zentrum für Lungenforschung (DZL), Giessen, Germany
- Pulmonary and Critical Care Medicine, University Medical Center Giessen and Marburg, Marburg, Germany
- German Center for Infectious Disease Research (DZIF), Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Zachary T. Ball
- Department of Chemistry, Rice University, Houston, Texas, USA
| | - Alexander Zarbock
- Department of Anesthesiology, Intensive Care and Pain Medicine, University Hospital Münster, Münster, Germany
| | - Mark R. Looney
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, School of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Jörg W. Bartsch
- Department of Neurosurgery/Lab, Faculty of Medicine, Philipps-University, Marburg, Germany
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8
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Clinical Evaluation of Pathognomonic Salivary Protease Fingerprinting for Oral Disease Diagnosis. J Pers Med 2021; 11:jpm11090866. [PMID: 34575643 PMCID: PMC8472161 DOI: 10.3390/jpm11090866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 08/26/2021] [Accepted: 08/26/2021] [Indexed: 11/22/2022] Open
Abstract
Dental decay (Caries) and periodontal disease are globally prevalent diseases with significant clinical need for improved diagnosis. As mediators of dental disease-specific extracellular matrix degradation, proteases are promising analytes. We hypothesized that dysregulation of active proteases can be functionally linked to oral disease status and may be used for diagnosis. To address this, we examined a total of 52 patients with varying oral disease states, including healthy controls. Whole mouth saliva samples and caries biopsies were collected and subjected to analysis. Overall proteolytic and substrate specific activities were assessed using five multiplexed, fluorogenic peptides. Peptide cleavage was further described by inhibitors targeting matrix metalloproteases (MMPs) and cysteine, serine, calpain proteases (CSC). Proteolytic fingerprints, supported by supervised machine-learning analysis, were delineated by total proteolytic activity (PepE) and substrate preference combined with inhibition profiles. Caries and peridontitis showed increased enzymatic activities of MMPs with common (PepA) and divergent substrate cleavage patterns (PepE), suggesting different MMP contribution in particular disease states. Overall, sensitivity and specificity values of 84.6% and 90.0%, respectively, were attained. Thus, a combined analysis of protease derived individual and arrayed substrate cleavage rates in conjunction with inhibitor profiles may represent a sensitive and specific tool for oral disease detection.
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9
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Yu D, Chen Y, Ahrens CC, Wang Y, Ding Z, Lim H, Fell C, Rumbaugh KP, Wu J, Li W. Direct monitoring of protease activity using an integrated microchip coated with multilayered fluorogenic nanofilms. Analyst 2021; 145:8050-8058. [PMID: 33073791 DOI: 10.1039/d0an01294g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Proteases play an essential role in the four sequential but overlapping phases of wound healing: hemostasis, inflammation, proliferation, and remodeling. In chronic wounds, excessive protease secretion damages the newly formed extracellular matrix, thereby delaying or preventing the normal healing process. Peptide-based fluorogenic sensors provide a visual platform to sense and analyze protease activity through changes in the fluorescence intensity. Here, we have developed an integrated microfluidic chip coated with multilayered fluorogenic nanofilms that can directly monitor protease activity. Fluorogenic protease sensors were chemically conjugated to polymer films coated on the surface of parallel microfluidic channels. Capillary flow layer-by-layer (CF-LbL) was used for film assembly and combined with subsequent sensor modification to establish a novel platform sensing technology. The benefits of our platform include facile fabrication and processing, controllable film nanostructure, small sample volume, and high sensitivity. We observed increased fluorescence of the LbL nanofilms when they were exposed to model recombinant proteases, confirming their responsiveness to protease activity. Increases in the nanofilms' fluorescence intensity were also observed during incubation with liquid extracted from murine infected wounds, demonstrating the potential of these films to provide real-time, in situ information about protease activity levels.
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Affiliation(s)
- Dan Yu
- Department of Critical Care Medicine, People's Hospital of Zhengzhou University (Henan Provincial People's Hospital), Zhengzhou, 450003, China
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10
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Vizovisek M, Ristanovic D, Menghini S, Christiansen MG, Schuerle S. The Tumor Proteolytic Landscape: A Challenging Frontier in Cancer Diagnosis and Therapy. Int J Mol Sci 2021; 22:ijms22052514. [PMID: 33802262 PMCID: PMC7958950 DOI: 10.3390/ijms22052514] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/24/2021] [Accepted: 02/25/2021] [Indexed: 02/06/2023] Open
Abstract
In recent decades, dysregulation of proteases and atypical proteolysis have become increasingly recognized as important hallmarks of cancer, driving community-wide efforts to explore the proteolytic landscape of oncologic disease. With more than 100 proteases currently associated with different aspects of cancer development and progression, there is a clear impetus to harness their potential in the context of oncology. Advances in the protease field have yielded technologies enabling sensitive protease detection in various settings, paving the way towards diagnostic profiling of disease-related protease activity patterns. Methods including activity-based probes and substrates, antibodies, and various nanosystems that generate reporter signals, i.e., for PET or MRI, after interaction with the target protease have shown potential for clinical translation. Nevertheless, these technologies are costly, not easily multiplexed, and require advanced imaging technologies. While the current clinical applications of protease-responsive technologies in oncologic settings are still limited, emerging technologies and protease sensors are poised to enable comprehensive exploration of the tumor proteolytic landscape as a diagnostic and therapeutic frontier. This review aims to give an overview of the most relevant classes of proteases as indicators for tumor diagnosis, current approaches to detect and monitor their activity in vivo, and associated therapeutic applications.
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11
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Wang X, Zhang D, Fucci QA, Dollery CM, Owen CA. Surface-bound matrix metalloproteinase-8 on macrophages: Contributions to macrophage pericellular proteolysis and migration through tissue barriers. Physiol Rep 2021; 9:e14778. [PMID: 33656791 PMCID: PMC7927794 DOI: 10.14814/phy2.14778] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 01/30/2021] [Accepted: 02/05/2021] [Indexed: 01/21/2023] Open
Abstract
Objective MMP‐8 binds to surface‐bound tissue inhibitor of metalloproteinase‐1 (TIMP‐1) on PMNs to promote pericellular proteolysis during the development of inflammatory diseases associated with tissue destruction. Little is known about the biology of MMP‐8 in macrophages. We tested the hypotheses that: (1) MMP‐8 and TIMP‐1 are also expressed on the surface of activated macrophages, (2) surface‐bound MMP‐8 on macrophages promotes TIMP‐resistant pericellular proteolysis and macrophage migration through tissue barriers, and (3) MMP‐8 binds to surface‐bound TIMP‐1 on macrophages. Methods Surface MMP‐8 and TIMP‐1 levels were measured on human monocyte‐derived macrophages (MDM) and/or murine macrophages using immunostaining, biotin‐labeling, and substrate cleavage methods. The susceptibility of membrane‐bound Mmp‐8 on activated macrophages from wild‐type (WT) mice to TIMPs was measured. Migration of WT and Mmp‐8−/− macrophages through models of tissue barriers in vitro and the accumulation of peritoneal macrophages in WT versus Mmp‐8−/− mice with sterile peritonitis was compared. Surface levels of Mmp‐8 were compared on activated macrophages from WT and Timp‐1−/− mice. Results Lipopolysaccharides and a cluster of differentiation 40 ligand increased surface MMP‐8 and/or TIMP‐1 staining and surface type I collagenase activity on MDM and/or murine macrophages. Activated Mmp‐8−/− macrophages degraded less type I collagen than activated WT macrophages. The surface type‐I collagenase activity on WT macrophages was resistant to inhibition by Timp‐1. Peritoneal macrophage accumulation was similar in WT and Mmp‐8−/− mice with sterile acute peritonitis. However, Mmp‐8−/− macrophages migrated less efficiently through models of tissue barriers (especially those containing type I collagen) than WT cells. Activated WT and Timp‐1−/− macrophages had similar surface‐bound Mmp‐8 levels. Conclusions MMP‐8 and TIMP‐1 are expressed on the surface of activated human MDM and murine macrophages, but Mmp‐8 is unlikely to bind to surface‐bound Timp‐1 on these cells. Surface‐bound MMP‐8 contributes to TIMP‐resistant monocyte/macrophage pericellular proteolysis and macrophage migration through collagen‐containing tissue barriers.
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Affiliation(s)
- Xiaoyun Wang
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Center for Vaccines and Immunology, University of Georgia, Athens, GA, USA.,Clinical and Experimental Therapeutics, College of Pharmacy, University of Georgia and Charlie Norwood VA Medical Center, Augusta, GA, USA
| | - Duo Zhang
- Clinical and Experimental Therapeutics, College of Pharmacy, University of Georgia and Charlie Norwood VA Medical Center, Augusta, GA, USA
| | - Quynh-Anh Fucci
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Clare M Dollery
- Whittington Hospital, Wittington Health NHS Trust, London, UK
| | - Caroline A Owen
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
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12
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Wang M, Nai MH, Huang RYJ, Leo HL, Lim CT, Chen CH. High-throughput functional profiling of single adherent cells via hydrogel drop-screen. LAB ON A CHIP 2021; 21:764-774. [PMID: 33506832 DOI: 10.1039/d0lc01294g] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Single-adherent-cell phenotyping on an extracellular matrix (ECM) is essential to determine cellular biological functions, such as morphological adaptations and biomolecule secretions, correlated to medical treatments and metastasis, yet there is no available platform for such high-throughput screening. Here, a novel hydrogel drop-screen device was developed to rapidly measure large-scale single-cell morphologies and multiple secretions on substrates for phenotype profiling. Single cells were first anchored to microfluidically fabricated gelatin particles providing mechanical stimulations similar to those from ECM in vivo. The cellular morphologies were then examined by quantifying the amount of cytoskeleton expressed on the particles. With droplet encapsulation, adherent single-cell multiplexed secretion analysis of a disintegrin and metalloproteinases (ADAMs) and matrix metalloproteinases (MMPs) was conducted at a throughput of ∼102 cells per second, revealing distinct functional heterogeneities associated with extracellular mechanical stimulations. The level of cell heterogeneity increased with increasing substrate stuffiness. Moreover, because of the promising screening capability, a database related to both nontumorigenic and tumorigenic breast cells (MCF10A, MCF-7, and MDA-MB-231) was constructed. The respective cell distributions and heterogeneities based on the morphologies and secreted bioindicators, such as MMP-2, MMP-3, MMP-9, and ADAM-8, were measured and found to correspond to the progress of tumor metastasis.
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Affiliation(s)
- Ming Wang
- NUS Graduate School for Integrative Sciences & Engineering, National University of Singapore, 21 Lower Kent Ridge Road, 119077 Singapore and Department of Biomedical Engineering, National University of Singapore, 4 Engineering Drive 3, 117583 Singapore and Institute for Health Innovation and Technology (iHealthtech), MD6, 14 Medical Drive 14-01, 117599 Singapore
| | - Mui Hoon Nai
- Department of Biomedical Engineering, National University of Singapore, 4 Engineering Drive 3, 117583 Singapore
| | - Ruby Yun-Ju Huang
- College of Medicine, National Taiwan University, No.1 Jen-Ai Road, Taipei, 10051, Taiwan and Graduate Institute of Oncology, College of Medicine, National Taiwan University, No. 1, Sec. 4, Roosevelt road, Taipei, 10617, Taiwan and Department of Biomedical Engineering, National Taiwan University, No.1, Sec.1, Jen-Ai Road, Taipei, 10051, Taiwan
| | - Hwa Liang Leo
- NUS Graduate School for Integrative Sciences & Engineering, National University of Singapore, 21 Lower Kent Ridge Road, 119077 Singapore and Department of Biomedical Engineering, National University of Singapore, 4 Engineering Drive 3, 117583 Singapore
| | - Chwee Teck Lim
- NUS Graduate School for Integrative Sciences & Engineering, National University of Singapore, 21 Lower Kent Ridge Road, 119077 Singapore and Department of Biomedical Engineering, National University of Singapore, 4 Engineering Drive 3, 117583 Singapore and Institute for Health Innovation and Technology (iHealthtech), MD6, 14 Medical Drive 14-01, 117599 Singapore and Mechanobiology Institute, National University of Singapore, 117411 Singapore
| | - Chia-Hung Chen
- Department of Biomedical Engineering, City University of Hong Kong, Y6700, 83 Tat Chee Avenue, Hong Kong SAR, China.
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13
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Wu W, Zhang S, Zhang T, Mu Y. Immobilized Droplet Arrays in Thermosetting Oil for Dynamic Proteolytic Assays of Single Cells. ACS APPLIED MATERIALS & INTERFACES 2021; 13:6081-6090. [PMID: 33504155 DOI: 10.1021/acsami.0c21696] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Matrix metalloproteinases (MMPs) play an important role in tumor progression. The study of dynamic MMPs activity at the single-cell level can dissect tumor heterogeneity in the time domain and facilitate finding out more efficient clinical solutions for tumor treatment. Due to the fluidity of the carrier oil, the existing droplet-based methods for single-cell MMP analysis rarely have the capability to track proteolytic assays in droplets continuously. Therefore, we describe a thermosetting oil for real-time monitoring of MMP assays in droplets, which can immobilize droplets by transforming into solid after droplet generation. The solidification of this oil can be accomplished in 33 min at 37 °C, basing on the hydrosilation of vinyl silicone oil and hydrosilicone oil without other inducers (e.g. UV, Ca2+). Through monitoring the MMP assays of single cells, the reaction rates can be calculated according to real-time fluorescent curves, showing significant cell heterogeneity in MMP activity. Moreover, the dynamic MMP activity reveals that some of the A549 cells transiently secrete MMP. In conclusion, the thermosetting oil enables immobilize droplets to achieve real-time monitoring of single-cell proteolytic activity without impairing the flexibility of droplet microfluidics and has a potential in other cell-based assays for providing dynamic information at high resolutions.
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Affiliation(s)
- Wenshuai Wu
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310027, P. R. China
- College of Life Sciences, Zhejiang University, Hangzhou 310058, P. R. China
| | - Shan Zhang
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310027, P. R. China
- College of Life Sciences, Zhejiang University, Hangzhou 310058, P. R. China
| | - Tao Zhang
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310027, P. R. China
| | - Ying Mu
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310027, P. R. China
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14
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Palau V, Riera M, Duran X, Valdivielso JM, Betriu A, Fernández E, Pascual J, Soler MJ. Circulating ADAMs are associated with renal and cardiovascular outcomes in chronic kidney disease patients. Nephrol Dial Transplant 2020; 35:130-138. [PMID: 30102333 DOI: 10.1093/ndt/gfy240] [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] [Received: 03/23/2018] [Accepted: 06/11/2018] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND A disintegrin and metalloproteinase (ADAM) 17, also known as tumour necrosis factor α-converting enzyme (TACE), is a metalloproteinase that releases the ectodomains of most growth factors, cytokines, receptors and enzymes and has been associated with the presence of chronic kidney disease (CKD) and cardiovascular (CV) disease. The role of circulating ADAMs in the progression of renal function and CV events in CKD patients is unknown. METHODS A total of 2570 subjects from an observational and multicentre study with CKD Stages 3-5, CKD Stage 5D and controls without any history of CV disease were studied. Circulating ADAM activity was assessed using a fluorometric technique. Progression of renal disease was defined as a 30% increase in serum creatinine or dialysis requirement after 24 months of follow-up. CV outcomes were assessed after 48 months of follow-up. RESULTS Patients with advanced CKD had higher ADAM activity as compared with patients with moderate CKD or controls. Male patients with progression of CKD had higher ADAM levels at baseline compared with patients with stable renal function {22.19 relative fluorescence units/μL/h [95% confidence interval (CI) 11.22-37.32] versus 12.15 (7.02-21.50)}. After multivariate adjustment, higher ADAM activity was identified as a risk factor for progression of CKD in male patients [30% increase in the creatinine odds ratio (OR) 2.72 (95% CI 1.58-4.68), P < 0.001; dialysis requirement OR 3.00 (95% CI 1.65-5.46), P < 0.001; dialysis requirement or 30% increase in the creatinine OR 3.15 (95% CI 2.06-4.81), P < 0.001]. ADAM activity was also identified as an independent risk factor for CV events [hazard ratio (HR) 1.68 (95% CI 1.20-2.36), P = 0.003]. CONCLUSIONS High ADAMs activity levels are independently associated with CKD progression in males and with CV events in CKD patients.
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Affiliation(s)
- Vanesa Palau
- Department of Nephrology, Hospital del Mar-Institut Hospital del Mar d'Investigacions Mèdiques, Barcelona, Spain
| | - Marta Riera
- Department of Nephrology, Hospital del Mar-Institut Hospital del Mar d'Investigacions Mèdiques, Barcelona, Spain
| | - Xavier Duran
- Institut Hospital del Mar d'Investigacions Mèdiques, Barcelona, Spain
| | - José Manuel Valdivielso
- Unit for Detection and Treatment of Atherothrombotic Diseases, Experimental Nephrology Laboratory, Arnau de Vilanova University Hospital, Biomedical Research Institute of Lleida, Lleida, Spain
| | - Angels Betriu
- Unit for Detection and Treatment of Atherothrombotic Diseases, Experimental Nephrology Laboratory, Arnau de Vilanova University Hospital, Biomedical Research Institute of Lleida, Lleida, Spain
| | - Elvira Fernández
- Unit for Detection and Treatment of Atherothrombotic Diseases, Experimental Nephrology Laboratory, Arnau de Vilanova University Hospital, Biomedical Research Institute of Lleida, Lleida, Spain
| | - Julio Pascual
- Department of Nephrology, Hospital del Mar-Institut Hospital del Mar d'Investigacions Mèdiques, Barcelona, Spain
| | - Maria José Soler
- Department of Nephrology, Hospital del Mar-Institut Hospital del Mar d'Investigacions Mèdiques, Barcelona, Spain
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15
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Gorry M, Yoneyama T, Vujanovic L, Moss ML, Garlin MA, Miller MA, Herman J, Stabile LP, Vujanovic NL. Development of flow cytometry assays for measuring cell-membrane enzyme activity on individual cells. J Cancer 2020; 11:702-715. [PMID: 31942194 PMCID: PMC6959049 DOI: 10.7150/jca.30813] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 09/12/2019] [Indexed: 02/06/2023] Open
Abstract
Background: Cell-membrane expressing enzymes such as ADAM (a disintegrin and metalloproteinase) superfamily members are thought to be key catalysts of vital cellular functions. To directly measure these enzymes and determine their association with particular cells and functions, individual-cell membrane-bound enzyme activity assays are required, but unavailable. Methods: We developed two such assays, using a fluorescence resonance energy transfer (FRET) peptide substrate (FPS) and flow cytometry. One assay measured live-cell natural processing of FPS and binding of its fluorescent product onto individual-cell membrane-bound enzymes. The other assay measured processing of specifically-bound and glutaraldehyde-crosslinked FPS, and consequent generation of its coupled fluorescent product onto individual-cell membrane-bound enzymes. Results: Confocal-microscopy imaging indicated that proteolytic processing of FPS selectively occurred on and labeled cell membrane of individual cells. The new assays measured specific increases of cell-associated FPS fluorescent product in substrate-concentration-, temperature- and time-dependent manners. A large proportion of processed FPS fluorescent products remained cell-associated after cell washing, indicating their binding to cell-membrane expressing enzymes. The assays measured higher levels of cell-associated FPS fluorescent product on wild-type than ADAM10-knockout mouse fibroblasts and on human monocytes than lymphocytes, which correlated with ADAM10 presence and expression levels on cell membrane, respectively. Furthermore, the enzyme activity assays could be combined with fluorescent anti-ADAM10 antibody staining to co-label and more directly associate enzyme activity and ADAM10 protein levels on cell membrane of individual cells. Conclusions: We report on two novel assays for measuring cell-membrane anchored enzyme activity on individual cells, and their potential use to directly study specific biology of cell-surface-expressing proteases.
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Affiliation(s)
- Michael Gorry
- University of Pittsburgh Cancer Institute, Pittsburgh, PA.,Department of Pathology, University of Pittsburgh.,VAPHS, Pittsburgh, PA
| | - Toshie Yoneyama
- University of Pittsburgh Cancer Institute, Pittsburgh, PA.,Department of Pathology, University of Pittsburgh.,VAPHS, Pittsburgh, PA
| | - Lazar Vujanovic
- University of Pittsburgh Cancer Institute, Pittsburgh, PA.,Department of Otolaryngology, University of Pittsburgh
| | | | - Michelle A Garlin
- Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Miles A Miller
- Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - James Herman
- University of Pittsburgh Cancer Institute, Pittsburgh, PA.,Department of Medicine, University of Pittsburgh
| | - Laura P Stabile
- University of Pittsburgh Cancer Institute, Pittsburgh, PA.,Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA
| | - Nikola L Vujanovic
- University of Pittsburgh Cancer Institute, Pittsburgh, PA.,Department of Pathology, University of Pittsburgh.,Department of Immunology, University of Pittsburgh.,VAPHS, Pittsburgh, PA
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16
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Single-cell proteolytic activity measurement using microfluidics for rare cell populations. Methods Enzymol 2019. [PMID: 31668226 DOI: 10.1016/bs.mie.2019.07.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Proteolytic degradation of the extracellular matrix represents a key step in cancer dissemination and metastasis. To probe cellular proteolytic activity, fluorescent sensing substrate was developed, yet prior studies focused on average activity of thousands of cells. Considerable evidence suggests a specialized subset of cancer cells are driving metastasis, highlighting the value of single-cell approach to reveal cancer cellular heterogeneity. In addition, when only a small number of cells are available, single-cell analysis is required to draw a statistical conclusion. Here, we present a microfluidic platform that provides high-efficiency cell loading and simple valveless isolation, so the proteolytic activity of a small number (10-100) of cells can be individually characterized. Furthermore, the platform allows monitoring single cells at multiple time points for the investigation of dynamics in proteolytic activity. The presented platform represents a simple and reliable tool for single-cell proteolytic analysis, illuminating the heterogeneous and dynamic nature of cancer cells.
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17
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Single-cell assays using integrated continuous-flow microfluidics. Methods Enzymol 2019. [PMID: 31668236 DOI: 10.1016/bs.mie.2019.06.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The recent maturation of continuous-flow microfluidic technologies has coincided with transformative new methods to profile single cells, including their genetic types, protein expression and enzyme activities. Continuous-flow high-throughput single-cell screening and sorting can reveal relationships across cellular phenotypes (e.g., enzyme activity and secretion) and genetic fingerprints. This technology provides unique opportunities, as well as experimental and computational challenges, for integrative approaches that can process large amounts of single-cell data. In this chapter, we discuss recent advances in integrated continuous-flow microfluidic approaches with a focus on measurements and statistical analysis of single-cell enzyme activity and their applications in quantitative biology, synthetic biology, and diagnosis.
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18
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Zhuang Q, Holt BA, Kwong GA, Qiu P. Deconvolving multiplexed protease signatures with substrate reduction and activity clustering. PLoS Comput Biol 2019; 15:e1006909. [PMID: 31479443 PMCID: PMC6743790 DOI: 10.1371/journal.pcbi.1006909] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 09/13/2019] [Accepted: 07/29/2019] [Indexed: 12/16/2022] Open
Abstract
Proteases are multifunctional, promiscuous enzymes that degrade proteins as well as peptides and drive important processes in health and disease. Current technology has enabled the construction of libraries of peptide substrates that detect protease activity, which provides valuable biological information. An ideal library would be orthogonal, such that each protease only hydrolyzes one unique substrate, however this is impractical due to off-target promiscuity (i.e., one protease targets multiple different substrates). Therefore, when a library of probes is exposed to a cocktail of proteases, each protease activates multiple probes, producing a convoluted signature. Computational methods for parsing these signatures to estimate individual protease activities primarily use an extensive collection of all possible protease-substrate combinations, which require impractical amounts of training data when expanding to search for more candidate substrates. Here we provide a computational method for estimating protease activities efficiently by reducing the number of substrates and clustering proteases with similar cleavage activities into families. We envision that this method will be used to extract meaningful diagnostic information from biological samples. The activity of enzymatic proteins, which are called proteases, drives numerous important processes in health and disease: including cancer, immunity, and infectious disease. Many labs have developed useful diagnostics by designing sensors that measure the activity of these proteases. However, if we want to detect multiple proteases at the same time, it becomes impractical to design sensors that only detect one protease. This is due to a phenomenon called protease promiscuity, which means that proteases will activate multiple different sensors. Computational methods have been created to solve this problem, but the challenge is that these often require large amounts of training data. Further, completely different proteases may be detected by the same subset of sensors. In this work, we design a computational method to overcome this problem by clustering similar proteases into "subfamilies", which increases estimation accuracy. Further, our method tests multiple combinations of sensors to maintain accuracy while minimizing the number of sensors used. Together, we envision that this work will increase the amount of useful information we can extract from biological samples, which may lead to better clinical diagnostics.
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Affiliation(s)
- Qinwei Zhuang
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Brandon Alexander Holt
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, Georgia, United States of America
| | - Gabriel A. Kwong
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, Georgia, United States of America
- Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- Institute for Electronics and Nanotechnology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- Integrated Cancer Research Center, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- Georgia ImmunoEngineering Consortium, Georgia Tech and Emory University, Atlanta, Georgia, United States of America
- * E-mail: (GAK); (PQ)
| | - Peng Qiu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, Georgia, United States of America
- Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- * E-mail: (GAK); (PQ)
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19
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Ahrens CC, Chiswick EL, Ravindra KC, Miller MA, Ramseier JY, Isaacson KB, Lauffenburger DA, Griffith LG. Development and Application of the Metalloprotease Activity Multiplexed Bead-Based Immunoassay (MAMBI). Biochemistry 2019; 58:3938-3942. [DOI: 10.1021/acs.biochem.9b00584] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Caroline C. Ahrens
- Department of Biological Engineering and Center for Gynepathology Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Evan L. Chiswick
- Department of Biological Engineering and Center for Gynepathology Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Kodihalli C. Ravindra
- Department of Biological Engineering and Center for Gynepathology Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Miles A. Miller
- Department of Biological Engineering and Center for Gynepathology Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Julie Y. Ramseier
- Department of Biological Engineering and Center for Gynepathology Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Keith B. Isaacson
- Department of Biological Engineering and Center for Gynepathology Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Minimally Invasive Gynecology Surgery Center, Newton Wellesley Hospital, Wellesley, Massachusetts 02462, United States
| | - Douglas A. Lauffenburger
- Department of Biological Engineering and Center for Gynepathology Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Linda G. Griffith
- Department of Biological Engineering and Center for Gynepathology Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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20
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ADAM8 in invasive cancers: links to tumor progression, metastasis, and chemoresistance. Clin Sci (Lond) 2019; 133:83-99. [PMID: 30635388 DOI: 10.1042/cs20180906] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 11/27/2018] [Accepted: 12/05/2018] [Indexed: 12/26/2022]
Abstract
Ectodomain shedding of extracellular and membrane proteins is of fundamental importance for cell-cell communication in neoplasias. A Disintegrin And Metalloproteinase (ADAM) proteases constitute a family of multifunctional, membrane-bound proteins with traditional sheddase functions. Their protumorigenic potential has been attributed to both, essential (ADAM10 and ADAM17) and 'dispensable' ADAM proteases (ADAM8, 9, 12, 15, and 19). Of specific interest in this review is the ADAM proteinase ADAM8 that has been identified as a significant player in aggressive malignancies including breast, pancreatic, and brain cancer. High expression levels of ADAM8 are associated with invasiveness and predict a poor patient outcome, indicating a prognostic and diagnostic potential of ADAM8. Current knowledge of substrates and interaction partners gave rise to the hypothesis that ADAM8 dysregulation affects diverse processes in tumor biology, attributable to different functional cores of the multidomain enzyme. Proteolytic degradation of extracellular matrix (ECM) components, cleavage of cell surface proteins, and subsequent release of soluble ectodomains promote cancer progression via induction of angiogenesis and metastasis. Moreover, there is increasing evidence for significance of a non-proteolytic function of ADAM8. With the disintegrin (DIS) domain ADAM8 binds integrins such as β1 integrin, thereby activating integrin signaling pathways. The cytoplasmic domain is critical for that activation and involves focal adhesion kinase (FAK), extracellular regulated kinase (ERK1/2), and protein kinase B (AKT/PKB) signaling, further contributing to cancer progression and mediating chemoresistance against first-line therapies. This review highlights the remarkable effects of ADAM8 in tumor biology, concluding that pharmacological inhibition of ADAM8 represents a promising therapeutic approach not only for monotherapy, but also for combinatorial therapies.
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21
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Oria VO, Lopatta P, Schmitz T, Preca BT, Nyström A, Conrad C, Bartsch JW, Kulemann B, Hoeppner J, Maurer J, Bronsert P, Schilling O. ADAM9 contributes to vascular invasion in pancreatic ductal adenocarcinoma. Mol Oncol 2019; 13:456-479. [PMID: 30556643 PMCID: PMC6360373 DOI: 10.1002/1878-0261.12426] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 11/16/2018] [Accepted: 12/03/2018] [Indexed: 12/17/2022] Open
Abstract
A disintegrin and a metalloprotease (ADAM)‐9 is a metzincin cell‐surface protease with strongly elevated expression in solid tumors, including pancreatic ductal adenocarcinoma (PDAC). In this study, we performed immunohistochemistry (IHC) of a tissue microarray (TMA) to examine the expression of ADAM9 in a cohort of >100 clinically annotated PDAC cases. We report that ADAM9 is prominently expressed by PDAC tumor cells, and increased ADAM9 expression levels correlate with poor tumor grading (P = 0.027) and the presence of vasculature invasion (P = 0.017). We employed gene expression silencing to generate a loss‐of‐function system for ADAM9 in two established PDAC cell lines. In vitro analysis showed that loss of ADAM9 does not impede cellular proliferation and invasiveness in basement membrane. However, ADAM9 plays a crucial role in mediating cell migration and adhesion to extracellular matrix substrates such as fibronectin, tenascin, and vitronectin. This effect appears to depend on its catalytic activity. In addition, ADAM9 facilitates anchorage‐independent growth. In AsPC1 cells, but not in MiaPaCa‐2 cells, we noted a pronounced yet heterogeneous impact of ADAM9 on the abundance of various integrins, a process that we characterized as post‐translational regulation. Sprout formation of human umbilical vein endothelial cells (HUVECs) is promoted by ADAM9, as examined by transfer of cancer cell conditioned medium; this finding further supports a pro‐angiogenic role of ADAM9 expressed by PDAC cancer cells. Immunoblotting analysis of cancer cell conditioned medium highlighted that ADAM9 regulates the levels of angiogenic factors, including shed heparin‐binding EGF‐like growth factor (HB‐EGF). Finally, we carried out orthotopic seeding of either wild‐type AsPC‐1 cells or AsPC‐1 cells with silenced ADAM9 expression into murine pancreas. In this in vivo setting, ADAM9 was also found to foster angiogenesis without an impact on tumor cell proliferation. In summary, our results characterize ADAM9 as an important regulator in PDAC tumor biology with a strong pro‐angiogenic impact.
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Affiliation(s)
- Victor O Oria
- Institute of Molecular Medicine and Cell Research, University of Freiburg, Germany.,Spemann Graduate School of Biology and Medicine, University of Freiburg, Germany.,Faculty of Biology, University of Freiburg, Germany
| | - Paul Lopatta
- Institute of Molecular Medicine and Cell Research, University of Freiburg, Germany
| | - Tatjana Schmitz
- Institute of Molecular Medicine and Cell Research, University of Freiburg, Germany
| | | | - Alexander Nyström
- Department of Dermatology, Medical Faculty, Medical Center - University of Freiburg, Germany
| | - Catharina Conrad
- Department of Neurosurgery, Philipps University Marburg, Germany.,Department of Anesthesiology, Intensive Care, and Pain Medicine, University of Münster, Germany
| | - Jörg W Bartsch
- Department of Neurosurgery, Philipps University Marburg, Germany
| | - Birte Kulemann
- Department of General and Visceral Surgery, Medical Center - University of Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Germany
| | - Jens Hoeppner
- Department of General and Visceral Surgery, Medical Center - University of Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Germany.,Comprehensive Cancer Center Freiburg, Medical Center - University of Freiburg, Germany
| | - Jochen Maurer
- Department of Gynecology, University Clinic RWTH, Aachen, Germany
| | - Peter Bronsert
- Faculty of Medicine, University of Freiburg, Germany.,Institute of Surgical Pathology, Medical Center - University of Freiburg, Germany.,German Cancer Consortium (DKTK) and Cancer Research Center (DKFZ), Heidelberg, Germany.,Tumorbank Comprehensive Cancer Center Freiburg, Medical Center - University of Freiburg, Germany
| | - Oliver Schilling
- Faculty of Medicine, University of Freiburg, Germany.,Institute of Surgical Pathology, Medical Center - University of Freiburg, Germany.,German Cancer Consortium (DKTK) and Cancer Research Center (DKFZ), Heidelberg, Germany.,Centre for Biological Signaling Studies BIOSS, University of Freiburg, Germany
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22
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Ng EX, Sun G, Wei SC, Miller MA, DasGupta R, Lam PYP, Chen CH. Ultrafast Single-Cell Level Enzymatic Tumor Profiling. Anal Chem 2018; 91:1277-1285. [DOI: 10.1021/acs.analchem.8b02576] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Ee Xien Ng
- Department of Biomedical Engineering, National University of Singapore, 4 Engineering Drive 3, 04-08, Singapore, Singapore
| | - Guoyun Sun
- Department of Biomedical Engineering, National University of Singapore, 4 Engineering Drive 3, 04-08, Singapore, Singapore
| | - Shih-Chung Wei
- Department of Biomedical Engineering, National University of Singapore, 4 Engineering Drive 3, 04-08, Singapore, Singapore
- Biomedical Institute for Global Health Research and Technology, Singapore, Singapore
| | - Miles A. Miller
- Center for Systems Biology, Massachusetts General Hospital, Boston, Massachusetts, United States
| | - Ramanuj DasGupta
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Paula Yeng Po Lam
- National Cancer Centre Singapore, 11 Hospital Drive, Singapore, Singapore
| | - Chia-Hung Chen
- Department of Biomedical Engineering, National University of Singapore, 4 Engineering Drive 3, 04-08, Singapore, Singapore
- Biomedical Institute for Global Health Research and Technology, Singapore, Singapore
- Singapore Institute for Neurotechnology, 28 Medical Dr. 05-COR, Singapore, Singapore
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23
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Yoneyama T, Gorry M, Sobo-Vujanovic A, Lin Y, Vujanovic L, Gaither-Davis A, Moss ML, Miller MA, Griffith LG, Lauffenburger DA, Stabile LP, Herman J, Vujanovic NL. ADAM10 Sheddase Activity is a Potential Lung-Cancer Biomarker. J Cancer 2018; 9:2559-2570. [PMID: 30026855 PMCID: PMC6036891 DOI: 10.7150/jca.24601] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 03/31/2018] [Indexed: 12/20/2022] Open
Abstract
Background: Increases in expression of ADAM10 and ADAM17 genes and proteins are inconsistently found in cancer lesions, and are not validated as clinically useful biomarkers. The enzyme-specific proteolytic activities, which are solely mediated by the active mature enzymes, directly reflect enzyme cellular functions and might be superior biomarkers than the enzyme gene or protein expressions, which comprise the inactive proenzymes and active and inactivated mature enzymes. Methods: Using a recent modification of the proteolytic activity matrix analysis (PrAMA) measuring specific enzyme activities in cell and tissue lysates, we examined the specific sheddase activities of ADAM10 (ADAM10sa) and ADAM17 (ADAM17sa) in human non-small cell lung-carcinoma (NSCLC) cell lines, patient primary tumors and blood exosomes, and the noncancerous counterparts. Results: NSCLC cell lines and patient tumors and exosomes consistently showed significant increases of ADAM10sa relative to their normal, inflammatory and/or benign-tumor controls. Additionally, stage IA-IIB NSCLC primary tumors of patients who died of the disease exhibited greater increases of ADAM10sa than those of patients who survived 5 years following diagnosis and surgery. In contrast, NSCLC cell lines and patient tumors and exosomes did not display increases of ADAM17sa. Conclusions: This study is the first to investigate enzyme-specific proteolytic activities as potential cancer biomarkers. It provides a proof-of-concept that ADAM10sa could be a biomarker for NSCLC early detection and outcome prediction. To ascertain that ADAM10sa is a useful cancer biomarker, further robust clinical validation studies are needed.
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Affiliation(s)
- Toshie Yoneyama
- Department of Pathology, University of Pittsburgh; UPMC Hillman Cancer Center, Pittsburgh, PA.,VAPHS, Pittsburgh, PA
| | - Michael Gorry
- Department of Pathology, University of Pittsburgh; UPMC Hillman Cancer Center, Pittsburgh, PA.,VAPHS, Pittsburgh, PA
| | - Andrea Sobo-Vujanovic
- Department of Pathology, University of Pittsburgh; UPMC Hillman Cancer Center, Pittsburgh, PA.,VAPHS, Pittsburgh, PA
| | - Yan Lin
- Department of Biostatistics, University of Pittsburgh; UPMC Hillman Cancer Center, Pittsburgh, PA
| | - Lazar Vujanovic
- Department of Medicine, University of Pittsburgh; UPMC Hillman Cancer Center, Pittsburgh, PA
| | - Autumn Gaither-Davis
- Department of Medicine, University of Pittsburgh; UPMC Hillman Cancer Center, Pittsburgh, PA
| | | | - Miles A Miller
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA
| | - Linda G Griffith
- Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Douglas A Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA.,Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Laura P Stabile
- Department of Pharmacology and Chemical Biology, University of Pittsburgh; UPMC Hillman Cancer Center, Pittsburgh, PA
| | - James Herman
- Department of Medicine, University of Pittsburgh; UPMC Hillman Cancer Center, Pittsburgh, PA
| | - Nikola L Vujanovic
- Department of Pathology, University of Pittsburgh; UPMC Hillman Cancer Center, Pittsburgh, PA.,Department of Immunology, University of Pittsburgh; UPMC Hillman Cancer Center, Pittsburgh, PA.,VAPHS, Pittsburgh, PA
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24
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Ravindra KC, Ahrens CC, Wang Y, Ramseier JY, Wishnok JS, Griffith LG, Grodzinsky AJ, Tannenbaum SR. Chemoproteomics of matrix metalloproteases in a model of cartilage degeneration suggests functional biomarkers associated with posttraumatic osteoarthritis. J Biol Chem 2018; 293:11459-11469. [PMID: 29794029 DOI: 10.1074/jbc.m117.818542] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 05/21/2018] [Indexed: 12/14/2022] Open
Abstract
Active matrix metalloproteases (MMPs) play a significant role in the pathogenesis of many diseases including osteoarthritis (OA), which involves progressive proteolytic degradation of cartilage. Clinical success of OA interventions that target MMPs has been limited by a lack of information about the presence and activity of specific disease-related proteases. We therefore developed a chemoproteomics approach based on MS to characterize the release and activity of MMPs in an in vitro model of the early inflammatory phase of posttraumatic OA (PTOA). We designed and synthesized chemical activity-based probes (ABPs) to identify active MMPs in bovine cartilage explants cultured for 30 days with the proinflammatory cytokine, interleukin-1α. Using these probes in an activity-based protein profiling-multidimensional identification technology (ABPP-MudPIT) approach, we identified active MMP-1, -2, -3, -7, -9, -12, and -13 in the medium after 10 days of culture, the time at which irreversible proteolysis of the collagen network in the explant was detected using proteolytic activation of FRET-quenched MMP substrates. Total MMP levels were quantified by shotgun proteomics, which, taken with ABPP-MudPIT data, indicated the presence of predominantly inactive MMPs in the culture medium. The selectivity of the ABPP-MudPIT approach was further validated by detection of specific endogenous MMPs activated de novo with 4-aminophenylmurcuric acetate. The utility of the new ABPP-MudPIT approach for detecting molecular biomarkers of PTOA disease initiation and potential targets for therapeutics motivates possible application in other diseases involving MMP activity.
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Affiliation(s)
- Kodihalli C Ravindra
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Caroline C Ahrens
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Yang Wang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Julie Y Ramseier
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - John S Wishnok
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Linda G Griffith
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139; Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139; Center for Gynepathology Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Alan J Grodzinsky
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139; Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139; Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Steven R Tannenbaum
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139.
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25
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Ripp S, Turunen P, Minot ED, Rowan AE, Blank KG. Deciphering Design Principles of Förster Resonance Energy Transfer-Based Protease Substrates: Thermolysin-Like Protease from Geobacillus stearothermophilus as a Test Case. ACS OMEGA 2018; 3:4148-4156. [PMID: 31458650 PMCID: PMC6641592 DOI: 10.1021/acsomega.7b02084] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 03/19/2018] [Indexed: 06/10/2023]
Abstract
Protease activity is frequently assayed using short peptides that are equipped with a Förster resonance energy transfer (FRET) reporter system. Many frequently used donor-acceptor pairs are excited in the ultraviolet range and suffer from low extinction coefficients and quantum yields, limiting their usefulness in applications where a high sensitivity is required. A large number of alternative chromophores are available that are excited in the visible range, for example, based on xanthene or cyanine core structures. These alternatives are not only larger in size but also more hydrophobic. Here, we show that the hydrophobicity of these chromophores not only affects the solubility of the resulting FRET-labeled peptides but also their kinetic parameters in a model enzymatic reaction. In detail, we have compared two series of 4-8 amino acid long peptides, designed to serve as substrates for the thermolysin-like protease (TLP-ste) from Geobacillus stearothermophilus. These peptides were equipped with a carboxyfluorescein donor and either Cy5 or its sulfonated derivative Alexa Fluor 647 as the acceptor. We show that the turnover rate k cat is largely unaffected by the choice of the acceptor fluorophore, whereas the K M value is significantly lower for the Cy5- than for the Alexa Fluor 647-labeled substrates. TLP-ste is a rather nonspecific protease with a large number of hydrophobic amino acids surrounding the catalytic site, so that the fluorophore itself may form additional interactions with the enzyme. This hypothesis is supported by the result that the difference between Cy5- and Alexa Fluor 647-labeled substrates becomes less pronounced with increasing peptide length, that is, when the fluorophore is positioned at a larger distance from the catalytic site. These results suggest that fluorophores may become an integral part of FRET-labeled peptide substrates and that K M and k cat values are generally only valid for a specific combination of the peptide sequence and FRET pair.
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Affiliation(s)
- Sophie Ripp
- Institute
for Molecules and Materials, Department of Molecular Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Petri Turunen
- Institute
for Molecules and Materials, Department of Molecular Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Ethan D. Minot
- Department
of Physics, Oregon State University, 301 Weniger Hall, Corvallis, Oregon 97331-6507, United States
| | - Alan E. Rowan
- Institute
for Molecules and Materials, Department of Molecular Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Kerstin G. Blank
- Institute
for Molecules and Materials, Department of Molecular Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
- Mechano(bio)chemistry,
Max Planck Institute of Colloids and Interfaces, Potsdam-Golm Science Park, 14424 Potsdam, Germany
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26
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Dudani JS, Warren AD, Bhatia SN. Harnessing Protease Activity to Improve Cancer Care. ANNUAL REVIEW OF CANCER BIOLOGY-SERIES 2018. [DOI: 10.1146/annurev-cancerbio-030617-050549] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jaideep S. Dudani
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;, ,
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Andrew D. Warren
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;, ,
- Harvard–MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Sangeeta N. Bhatia
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;, ,
- Harvard–MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02139, USA
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27
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Conrad C, Götte M, Schlomann U, Roessler M, Pagenstecher A, Anderson P, Preston J, Pruessmeyer J, Ludwig A, Li R, Kamm RD, Ritz R, Carl B, Nimsky C, Bartsch JW. ADAM8 expression in breast cancer derived brain metastases: Functional implications on MMP-9 expression and transendothelial migration in breast cancer cells. Int J Cancer 2017; 142:779-791. [DOI: 10.1002/ijc.31090] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 08/14/2017] [Accepted: 09/18/2017] [Indexed: 12/30/2022]
Affiliation(s)
- Catharina Conrad
- Department of Neurosurgery; Philipps University Marburg, Baldingerstr; Marburg, 35033 Germany
- Department of Anesthesiology; Intensive Care, and Pain Medicine, University of Münster, Albert-Schweitzer Campus 1; Münster 48149 Germany
| | - Malena Götte
- Department of Neurosurgery; Philipps University Marburg, Baldingerstr; Marburg, 35033 Germany
| | - Uwe Schlomann
- Department of Neurosurgery; Philipps University Marburg, Baldingerstr; Marburg, 35033 Germany
| | - Marion Roessler
- Department of Pathology; Philipps University Marburg, Baldingerstr; Marburg 35033 Germany
| | - Axel Pagenstecher
- Department of Neuropathology; Philipps University Marburg, Baldingerstr; Marburg 35033 Germany
| | - Peter Anderson
- King's College London, Institute of Pharmaceutical Science, 150 Stamford Street; London SE1 9NH United Kingdom
| | - Jane Preston
- King's College London, Institute of Pharmaceutical Science, 150 Stamford Street; London SE1 9NH United Kingdom
| | | | - Andreas Ludwig
- Institute for Pharmacological Research, Aachen University; Aachen Germany
| | - Ran Li
- MIT Department of Biological Engineering; Cambridge MA
| | - Roger D. Kamm
- MIT Department of Biological Engineering; Cambridge MA
| | - Rainer Ritz
- Department of Neurosurgery; Philipps University Marburg, Baldingerstr; Marburg, 35033 Germany
| | - Barbara Carl
- Department of Neurosurgery; Philipps University Marburg, Baldingerstr; Marburg, 35033 Germany
| | - Christopher Nimsky
- Department of Neurosurgery; Philipps University Marburg, Baldingerstr; Marburg, 35033 Germany
| | - Jörg W. Bartsch
- Department of Neurosurgery; Philipps University Marburg, Baldingerstr; Marburg, 35033 Germany
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28
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Yoneyama T, Gorry M, Miller MA, Gaither-Davis A, Lin Y, Moss ML, Griffith LG, Lauffenburger DA, Stabile LP, Herman JG, Vujanovic NL. Modification of proteolytic activity matrix analysis (PrAMA) to measure ADAM10 and ADAM17 sheddase activities in cell and tissue lysates. J Cancer 2017; 8:3916-3932. [PMID: 29187866 PMCID: PMC5705993 DOI: 10.7150/jca.20779] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 08/06/2017] [Indexed: 01/29/2023] Open
Abstract
Increases in expression of ADAM10 and ADAM17 genes and proteins have been evaluated, but not validated as cancer biomarkers. Specific enzyme activities better reflect enzyme cellular functions, and might be better biomarkers than enzyme genes or proteins. However, no high throughput assay is available to test this possibility. Recent studies have developed the high throughput real-time proteolytic activity matrix analysis (PrAMA) that integrates the enzymatic processing of multiple enzyme substrates with mathematical-modeling computation. The original PrAMA measures with significant accuracy the activities of individual metalloproteinases expressed on live cells. To make the biomarker assay usable in clinical practice, we modified PrAMA by testing enzymatic activities in cell and tissue lysates supplemented with broad-spectrum non-MP enzyme inhibitors, and by maximizing the assay specificity using systematic mathematical-modeling analyses. The modified PrAMA accurately measured the absence and decreases of ADAM10 sheddase activity (ADAM10sa) and ADAM17sa in ADAM10-/- and ADAM17-/- mouse embryonic fibroblasts (MEFs), and ADAM10- and ADAM17-siRNA transfected human cancer cells, respectively. It also measured the restoration and inhibition of ADAM10sa in ADAM10-cDNA-transfected ADAM10-/- MEFs and GI254023X-treated human cancer cell and tissue lysates, respectively. Additionally, the modified PrAMA simultaneously quantified with significant accuracy ADAM10sa and ADAM17sa in multiple human tumor specimens, and showed the essential characteristics of a robust high throughput multiplex assay that could be broadly used in biomarker studies. Selectively measuring specific enzyme activities, this new clinically applicable assay is potentially superior to the standard protein- and gene-expression assays that do not distinguish active and inactive enzyme forms.
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Affiliation(s)
- Toshie Yoneyama
- Department of Pathology, University of Pittsburgh Cancer Institute, Pittsburgh, PA.,VAPHS, Pittsburgh, PA
| | - Michael Gorry
- Department of Pathology, University of Pittsburgh Cancer Institute, Pittsburgh, PA.,VAPHS, Pittsburgh, PA
| | - Miles A Miller
- Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Autumn Gaither-Davis
- Department of Medicine, University of Pittsburgh Cancer Institute, Pittsburgh, PA
| | - Yan Lin
- Department of Biostatistics, University of Pittsburgh Cancer Institute, Pittsburgh, PA
| | | | - Linda G Griffith
- Department of Biologic Engineering, Massachusetts Institute of Technology
| | | | - Laura P Stabile
- Department of Pharmacology and Chemical Biology, University of Pittsburgh Cancer Institute, Pittsburgh, PA
| | - James G Herman
- Department of Medicine, University of Pittsburgh Cancer Institute, Pittsburgh, PA
| | - Nikola L Vujanovic
- Department of Pathology, University of Pittsburgh Cancer Institute, Pittsburgh, PA.,Department of Immunology, University of Pittsburgh Cancer Institute, Pittsburgh, PA.,VAPHS, Pittsburgh, PA
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29
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Conrad C, Dorzweiler K, Miller MA, Lauffenburger DA, Strik H, Bartsch JW. Profiling of metalloprotease activities in cerebrospinal fluids of patients with neoplastic meningitis. Fluids Barriers CNS 2017; 14:22. [PMID: 28806983 PMCID: PMC5556623 DOI: 10.1186/s12987-017-0070-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 08/03/2017] [Indexed: 12/15/2022] Open
Abstract
Background Neoplastic invasion into leptomeninges and subarachnoid space, resulting in neoplastic meningitis (NM) is a fatal complication of advanced solid and hematological neoplasms. Identification of malignant involvement of the cerebrospinal fluid (CSF) early in the disease course has crucial prognostic and therapeutic implications, but remains challenging. As indicators of extracellular matrix (ECM) degradation and breakdown of the blood–brain-barrier, Matrix Metalloproteases (MMPs) and A Disintegrin and Metalloproteases (ADAMs) are potential analytes for cerebral pathophysiology and metastatic dissemination of tumor cells into the CSF. Methods We compared protease activities in CSF samples from patients with NM and control individuals using FRET-based metalloprotease substrates with distinct enzyme selectivity profiles in a real-time, multiplex approach termed “proteolytic activity matrix assay” (PrAMA). Protease activity dynamics can be tracked by fluorescence changes over time. By simultaneously monitoring a panel of 5 FRET-substrate cleavages, a proteolytic signature can be identified and analyzed to infer the activities of multiple specific proteases. Distinct patterns of substrate cleavage comparing disease vs. control samples allow rapid, reproducible and sensitive discrimination even in small volumes of CSF. Results Individual substrate cleavage rates were linked to distinct proteases, and PrAMA computational inference implied increased activities of MMP-9, ADAM8 and ADAM17 (4–5-fold on average) in CSF samples from NM patients that were inhibitable by the metalloprotease inhibitor batimastat (BB-94). The activities of these proteases correlated with blood–brain barrier impairment. Notably, CSF cell counts were not found to directly reflect the protease activities observed in CSF samples from NM patients; this may explain the frequent clinical observation of negative cytology in NM patients. Conclusion PrAMA analysis of CSF samples is a potential diagnostic method for sensitive detection of NM and may be suitable for the clinical routine. Electronic supplementary material The online version of this article (doi:10.1186/s12987-017-0070-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Catharina Conrad
- Department of Neurology, Philipps University Marburg, Baldingerstr, 35033, Marburg, Germany.,Department of Anesthesiology and Intensive Care Medicine, University Hospital, Albert-Schweitzer Campus 1, 48149, Münster, Germany
| | - Kristina Dorzweiler
- Department of Neurosurgery, Philipps University Marburg, Baldingerstr, 35033, Marburg, Germany
| | - Miles A Miller
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Douglas A Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Herwig Strik
- Department of Neurology, Philipps University Marburg, Baldingerstr, 35033, Marburg, Germany.
| | - Jörg W Bartsch
- Department of Neurosurgery, Philipps University Marburg, Baldingerstr, 35033, Marburg, Germany.
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30
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Levin M, Udi Y, Solomonov I, Sagi I. Next generation matrix metalloproteinase inhibitors - Novel strategies bring new prospects. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2017. [PMID: 28636874 DOI: 10.1016/j.bbamcr.2017.06.009] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Enzymatic proteolysis of cell surface proteins and extracellular matrix (ECM) is critical for tissue homeostasis and cell signaling. These proteolytic activities are mediated predominantly by a family of proteases termed matrix metalloproteinases (MMPs). The growing evidence in recent years that ECM and non-ECM bioactive molecules (e.g., growth factors, cytokines, chemokines, on top of matrikines and matricryptins) have versatile functions redefines our view on the roles matrix remodeling enzymes play in many physiological and pathological processes, and underscores the notion that ECM proteolytic reaction mechanisms represent master switches in the regulation of critical biological processes and govern cell behavior. Accordingly, MMPs are not only responsible for direct degradation of ECM molecules but are also key modulators of cardinal bioactive factors. Many attempts were made to manipulate ECM degradation by targeting MMPs using small peptidic and organic inhibitors. However, due to the high structural homology shared by these enzymes, the majority of the developed compounds are broad-spectrum inhibitors affecting the proteolytic activity of various MMPs and other zinc-related proteases. These inhibitors, in many cases, failed as therapeutic agents, mainly due to the bilateral role of MMPs in pathological conditions such as cancer, in which MMPs have both pro- and anti-tumorigenic effects. Despite the important role of MMPs in many human diseases, none of the broad-range synthetic MMP inhibitors that were designed have successfully passed clinical trials. It appears that, designing highly selective MMP inhibitors that are also effective in vivo, is not trivial. The challenges related to designing selective and effective metalloprotease inhibitors, are associated in part with the aforesaid high structural homology and the dynamic nature of their protein scaffolds. Great progress was achieved in the last decade in understanding the biochemistry and biology of MMPs activity. This knowledge, combined with lessons from the past has drawn new "boundaries" for the development of the next-generation MMP inhibitors. These novel agents are currently designed to be highly specific, capable to discriminate between the homologous MMPs and ideally administered as a short-term topical treatment. In this review we discuss the latest progress in the fields of MMP inhibitors in terms of structure, function and their specific activity. The development of novel highly specific inhibitors targeting MMPs paves the path to study complex biological processes associated with ECM proteolysis in health and disease. This article is part of a Special Issue entitled: Matrix Metalloproteinases edited by Rafael Fridman.
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Affiliation(s)
- Maxim Levin
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yael Udi
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA
| | - Inna Solomonov
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Irit Sagi
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel.
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31
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Lei Z, Zhang H, Wang Y, Meng X, Wang Z. Peptide Microarray-Based Metal Enhanced Fluorescence Assay for Multiple Profiling of Matrix Metalloproteinases Activities. Anal Chem 2017; 89:6749-6757. [DOI: 10.1021/acs.analchem.7b01037] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Zhen Lei
- State Key Laboratory
of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Hua Zhang
- State Key Laboratory
of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China
| | - Yaoqi Wang
- Department
of Thyroid Surgery, The First Hospital of Jilin University, Changchun, Jilin 130021, P. R. China
| | - Xianying Meng
- Department
of Thyroid Surgery, The First Hospital of Jilin University, Changchun, Jilin 130021, P. R. China
| | - Zhenxin Wang
- State Key Laboratory
of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China
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32
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Kwon EJ, Dudani JS, Bhatia SN. Ultrasensitive tumour-penetrating nanosensors of protease activity. Nat Biomed Eng 2017; 1:0054. [PMID: 28970963 PMCID: PMC5621765 DOI: 10.1038/s41551-017-0054] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Accepted: 03/01/2017] [Indexed: 12/25/2022]
Abstract
The ability to identify cancer lesions with endogenous biomarkers is currently limited to tumours ~1 cm in diameter. We recently reported an exogenously administered tumour-penetrating nanosensor that sheds, in response to tumour-specific proteases, peptide fragments that can then be detected in the urine. Here, we report the optimization, informed by a pharmacokinetic mathematical model, of the surface presentation of the peptide substrates to both enhance on-target protease cleavage and minimize off-target cleavage, and of the functionalization of the nanosensors with tumour-penetrating ligands that engage active trafficking pathways to increase activation in the tumour microenvironment. The resulting nanosensor discriminated sub-5 mm lesions in human epithelial tumours and detected nodules with median diameters smaller than 2 mm in an orthotopic model of ovarian cancer. We also demonstrate enhanced receptor-dependent specificity of signal generation in the urine in an immunocompetent model of colorectal liver metastases, and in situ activation of the nanosensors in human tumour microarrays when re-engineered as fluorogenic zymography probes.
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Affiliation(s)
- Ester J. Kwon
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
- Harvard–MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Jaideep S. Dudani
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Sangeeta N. Bhatia
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
- Harvard–MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02139
- Howard Hughes Medical Institute, Cambridge, MA 02139
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Miller MA, Weissleder R. Imaging the pharmacology of nanomaterials by intravital microscopy: Toward understanding their biological behavior. Adv Drug Deliv Rev 2017; 113:61-86. [PMID: 27266447 PMCID: PMC5136524 DOI: 10.1016/j.addr.2016.05.023] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 05/25/2016] [Indexed: 12/15/2022]
Abstract
Therapeutic nanoparticles (NPs) can deliver cytotoxic chemotherapeutics and other drugs more safely and efficiently to patients; furthermore, selective delivery to target tissues can theoretically be accomplished actively through coating NPs with molecular ligands, and passively through exploiting physiological "enhanced permeability and retention" features. However, clinical trial results have been mixed in showing improved efficacy with drug nanoencapsulation, largely due to heterogeneous NP accumulation at target sites across patients. Thus, a clear need exists to better understand why many NP strategies fail in vivo and not result in significantly improved tumor uptake or therapeutic response. Multicolor in vivo confocal fluorescence imaging (intravital microscopy; IVM) enables integrated pharmacokinetic and pharmacodynamic (PK/PD) measurement at the single-cell level, and has helped answer key questions regarding the biological mechanisms of in vivo NP behavior. This review summarizes progress to date and also describes useful technical strategies for successful IVM experimentation.
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Affiliation(s)
- Miles A Miller
- Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge St, Boston, MA 02114, USA
| | - Ralph Weissleder
- Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge St, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, 200 Longwood Ave, Boston, MA 02115, USA.
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34
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Conrad C, Miller MA, Bartsch JW, Schlomann U, Lauffenburger DA. Simultaneous Detection of Metalloprotease Activities in Complex Biological Samples Using the PrAMA (Proteolytic Activity Matrix Assay) Method. Methods Mol Biol 2017; 1574:243-253. [PMID: 28315256 DOI: 10.1007/978-1-4939-6850-3_18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Proteolytic Activity Matrix Analysis (PrAMA) is a method for simultaneously determining the activities of specific Matrix Metalloproteinases (MMPs) and A Disintegrin and Metalloproteinases (ADAMs) in complex biological samples. In mixtures of unknown proteases, PrAMA infers selective metalloproteinase activities by using a panel of moderately specific FRET-based polypeptide protease substrates in parallel, typically monitored by a plate-reader in a 96-well format. Fluorescence measurements are then quantitatively compared to a standard table of catalytic efficiencies measured from purified mixtures of individual metalloproteinases and FRET substrates. Computational inference of specific activities is performed with an easily used Matlab program, which is provided herein. Thus, we describe PrAMA as a combined experimental and mathematical approach to determine real-time metalloproteinase activities, which has previously been applied to live-cell cultures, cellular lysates, cell culture supernatants, and body fluids from patients.
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Affiliation(s)
- Catharina Conrad
- Department of Neurosurgery, Marburg University, 35033, Marburg, Germany
- Department of Anesthesiology and Intensive Care Medicine, University Hospital, Albert-Schweitzer Campus 1, 48149, Münster, Germany
| | - Miles A Miller
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Jörg W Bartsch
- Department of Neurosurgery, Marburg University, 35033, Marburg, Germany.
| | - Uwe Schlomann
- Department of Neurosurgery, Marburg University, 35033, Marburg, Germany
| | - Douglas A Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
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35
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Padamsey Z, McGuinness L, Bardo SJ, Reinhart M, Tong R, Hedegaard A, Hart ML, Emptage NJ. Activity-Dependent Exocytosis of Lysosomes Regulates the Structural Plasticity of Dendritic Spines. Neuron 2016; 93:132-146. [PMID: 27989455 PMCID: PMC5222721 DOI: 10.1016/j.neuron.2016.11.013] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 09/02/2016] [Accepted: 10/31/2016] [Indexed: 11/28/2022]
Abstract
Lysosomes have traditionally been viewed as degradative organelles, although a growing body of evidence suggests that they can function as Ca2+ stores. Here we examined the function of these stores in hippocampal pyramidal neurons. We found that back-propagating action potentials (bpAPs) could elicit Ca2+ release from lysosomes in the dendrites. This Ca2+ release triggered the fusion of lysosomes with the plasma membrane, resulting in the release of Cathepsin B. Cathepsin B increased the activity of matrix metalloproteinase 9 (MMP-9), an enzyme involved in extracellular matrix (ECM) remodelling and synaptic plasticity. Inhibition of either lysosomal Ca2+ signaling or Cathepsin B release prevented the maintenance of dendritic spine growth induced by Hebbian activity. This impairment could be rescued by exogenous application of active MMP-9. Our findings suggest that activity-dependent exocytosis of Cathepsin B from lysosomes regulates the long-term structural plasticity of dendritic spines by triggering MMP-9 activation and ECM remodelling. Back-propagating action potentials induce Ca2+ release from lysosomes in neurons Lysosomal Ca2+ release triggers exocytosis of the lysosomal protease Cathepsin B Cathepsin B maintains activity-dependent dendritic spine growth by activating MMP-9
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Affiliation(s)
- Zahid Padamsey
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK
| | - Lindsay McGuinness
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK
| | - Scott J Bardo
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK
| | - Marcia Reinhart
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK
| | - Rudi Tong
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK
| | - Anne Hedegaard
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK
| | - Michael L Hart
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK
| | - Nigel J Emptage
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK.
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36
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Schuerle S, Dudani JS, Christiansen MG, Anikeeva P, Bhatia SN. Magnetically Actuated Protease Sensors for in Vivo Tumor Profiling. NANO LETTERS 2016; 16:6303-6310. [PMID: 27622711 PMCID: PMC5344125 DOI: 10.1021/acs.nanolett.6b02670] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Targeted cancer therapies require a precise determination of the underlying biological processes driving tumorigenesis within the complex tumor microenvironment. Therefore, new diagnostic tools that capture the molecular activity at the disease site in vivo are needed to better understand tumor behavior and ultimately maximize therapeutic responses. Matrix metalloproteinases (MMPs) drive multiple aspects of tumorigenesis, and their activity can be monitored using engineered peptide substrates as protease-specific probes. To identify tumor specific activity profiles, local sampling of the tumor microenvironment is necessary, such as through remote control of probes, which are only activated at the tumor site. Alternating magnetic fields (AMFs) provide an attractive option to remotely apply local triggering signals because they penetrate deep into the body and are not likely to interfere with biological processes due to the weak magnetic properties of tissue. Here, we report the design and evaluation of a protease-activity nanosensor that can be remotely activated at the site of disease via an AMF at 515 kHz and 15 kA/m. Our nanosensor was composed of thermosensitive liposomes containing functionalized protease substrates that were unveiled at the target site by remotely triggered heat dissipation of coencapsulated magnetic nanoparticles (MNPs). This nanosensor was combined with a unique detection assay to quantify the amount of cleaved substrates in the urine. We applied this spatiotemporally controlled system to determine tumor protease activity in vivo and identified differences in substrate cleavage profiles between two mouse models of human colorectal cancer.
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Affiliation(s)
- Simone Schuerle
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Jaideep S. Dudani
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Michael G. Christiansen
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Polina Anikeeva
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Corresponding Authors: Address: Massachusetts Institute of Technology, 77 Massachusetts Avenue, Building 76-453, Cambridge, MA 02139, USA. Phone: + 1 617 324 0610, ; Address: Massachusetts Institute of Technology, 77 Massachusetts Avenue, Building 8-425, Cambridge, MA 02139, USA. Phone: + 1 617-253-3301,
| | - Sangeeta N. Bhatia
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139
- Marble Center for Cancer Nanomedicine, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02139
- Howard Hughes Medical Institute, Cambridge, MA 02139
- Corresponding Authors: Address: Massachusetts Institute of Technology, 77 Massachusetts Avenue, Building 76-453, Cambridge, MA 02139, USA. Phone: + 1 617 324 0610, ; Address: Massachusetts Institute of Technology, 77 Massachusetts Avenue, Building 8-425, Cambridge, MA 02139, USA. Phone: + 1 617-253-3301,
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37
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Moss ML, Minond D, Yoneyama T, Hansen HP, Vujanovic N, Rasmussen FH. An improved fluorescent substrate for assaying soluble and membrane-associated ADAM family member activities. Anal Biochem 2016; 507:13-7. [PMID: 27177841 DOI: 10.1016/j.ab.2016.05.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 04/21/2016] [Accepted: 05/01/2016] [Indexed: 10/21/2022]
Abstract
A fluorescent resonance energy transfer substrate with improved sensitivity for ADAM17, -10, and -9 (where ADAM represents a disintegrin and metalloproteinase) has been designed. The new substrate, Dabcyl-Pro-Arg-Ala-Ala-Ala-Homophe-Thr-Ser-Pro-Lys(FAM)-NH2, has specificity constants of 6.3 (±0.3) × 10(4) M(-1) s(-1) and 2.4 (±0.3) × 10(3) M(-1) s(-1) for ADAM17 and ADAM10, respectively. The substrate is more sensitive than widely used peptides based on the precursor tumor necrosis factor-alpha (TNF-alpha) cleavage site, PEPDAB010 or Dabcyl-Ser-Pro-Leu-Ala-Gln-Ala-Val-Arg-Ser-Ser-Lys(FAM)-NH2 and Mca-Pro-Leu-Ala-Gln-Ala-Val-Dpa-Arg-Ser-Ser-Arg-NH2. ADAM9 also processes the new peptide more than 18-fold better than the TNF-alpha-based substrates. The new substrate has a unique selectivity profile because it is processed less efficiently by ADAM8 and MMP1, -2, -3, -8, -9, -12, and -14. This substrate provides a unique tool in which to assess ADAM17, -10, and -9 activities.
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Affiliation(s)
| | - Dmitriy Minond
- Department of Drug Discovery and Development, Harrison School of Pharmacy, Auburn University, Auburn, AL 36849, USA
| | - Toshie Yoneyama
- Department of Pathology, University of Pittsburgh Cancer Institute, VA Healthcare System, Pittsburgh, PA 15232, USA
| | - Hinrich P Hansen
- Department of Internal Medicine I, University Clinic Cologne, Cologne 50937, Germany
| | - Nikola Vujanovic
- Department of Pathology, University of Pittsburgh Cancer Institute, VA Healthcare System, Pittsburgh, PA 15232, USA
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38
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Abstract
Clustering is an unsupervised learning method, which groups data points based on similarity, and is used to reveal the underlying structure of data. This computational approach is essential to understanding and visualizing the complex data that are acquired in high-throughput multidimensional biological experiments. Clustering enables researchers to make biological inferences for further experiments. Although a powerful technique, inappropriate application can lead biological researchers to waste resources and time in experimental follow-up. We review common pitfalls identified from the published molecular biology literature and present methods to avoid them. Commonly encountered pitfalls relate to the high-dimensional nature of biological data from high-throughput experiments, the failure to consider more than one clustering method for a given problem, and the difficulty in determining whether clustering has produced meaningful results. We present concrete examples of problems and solutions (clustering results) in the form of toy problems and real biological data for these issues. We also discuss ensemble clustering as an easy-to-implement method that enables the exploration of multiple clustering solutions and improves robustness of clustering solutions. Increased awareness of common clustering pitfalls will help researchers avoid overinterpreting or misinterpreting the results and missing valuable insights when clustering biological data.
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Affiliation(s)
- Tom Ronan
- Department of Biomedical Engineering, Center for Biological Systems Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Zhijie Qi
- Department of Biomedical Engineering, Center for Biological Systems Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Kristen M Naegle
- Department of Biomedical Engineering, Center for Biological Systems Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA.
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39
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Chen YC, Cheng YH, Ingram P, Yoon E. Single Cell Proteolytic Assays to Investigate Cancer Clonal Heterogeneity and Cell Dynamics Using an Efficient Cell Loading Scheme. Sci Rep 2016; 6:27154. [PMID: 27283981 PMCID: PMC4901291 DOI: 10.1038/srep27154] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 05/03/2016] [Indexed: 02/07/2023] Open
Abstract
Proteolytic degradation of the extracellular matrix (ECM) is critical in cancer invasion, and recent work suggests that heterogeneous cancer populations cooperate in this process. Despite the importance of cell heterogeneity, conventional proteolytic assays measure average activity, requiring thousands of cells and providing limited information about heterogeneity and dynamics. Here, we developed a microfluidic platform that provides high-efficiency cell loading and simple valveless isolation, so the proteolytic activity of a small sample (10-100 cells) can be easily characterized. Combined with a single cell derived (clonal) sphere formation platform, we have successfully demonstrated the importance of microenvironmental cues for proteolytic activity and also investigated the difference between clones. Furthermore, the platform allows monitoring single cells at multiple time points, unveiling different cancer cell line dynamics in proteolytic activity. The presented tool facilitates single cell proteolytic analysis using small samples, and our findings illuminate the heterogeneous and dynamic nature of proteolytic activity.
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Affiliation(s)
- Yu-Chih Chen
- Department of Electrical Engineering and Computer Science, University of Michigan, 1301 Beal Avenue, Ann Arbor, MI 48109-2122, USA
- University of Michigan Comprehensive Cancer Center, 1500 E. Medical Center Drive, Ann Arbor, MI 48109, USA
| | - Yu-Heng Cheng
- Department of Electrical Engineering and Computer Science, University of Michigan, 1301 Beal Avenue, Ann Arbor, MI 48109-2122, USA
| | - Patrick Ingram
- Department of Biomedical Engineering, University of Michigan, 2200 Bonisteel, Blvd. Ann Arbor, MI 48109-2099, USA
| | - Euisik Yoon
- Department of Electrical Engineering and Computer Science, University of Michigan, 1301 Beal Avenue, Ann Arbor, MI 48109-2122, USA
- Department of Biomedical Engineering, University of Michigan, 2200 Bonisteel, Blvd. Ann Arbor, MI 48109-2099, USA
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40
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Miller MA, Oudin MJ, Sullivan RJ, Wang SJ, Meyer AS, Im H, Frederick DT, Tadros J, Griffith LG, Lee H, Weissleder R, Flaherty KT, Gertler FB, Lauffenburger DA. Reduced Proteolytic Shedding of Receptor Tyrosine Kinases Is a Post-Translational Mechanism of Kinase Inhibitor Resistance. Cancer Discov 2016; 6:382-99. [PMID: 26984351 DOI: 10.1158/2159-8290.cd-15-0933] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 02/17/2016] [Indexed: 12/17/2022]
Abstract
UNLABELLED Kinase inhibitor resistance often involves upregulation of poorly understood "bypass" signaling pathways. Here, we show that extracellular proteomic adaptation is one path to bypass signaling and drug resistance. Proteolytic shedding of surface receptors, which can provide negative feedback on signaling activity, is blocked by kinase inhibitor treatment and enhances bypass signaling. In particular, MEK inhibition broadly decreases shedding of multiple receptor tyrosine kinases (RTK), including HER4, MET, and most prominently AXL, an ADAM10 and ADAM17 substrate, thus increasing surface RTK levels and mitogenic signaling. Progression-free survival of patients with melanoma treated with clinical BRAF/MEK inhibitors inversely correlates with RTK shedding reduction following treatment, as measured noninvasively in blood plasma. Disrupting protease inhibition by neutralizing TIMP1 improves MAPK inhibitor efficacy, and combined MAPK/AXL inhibition synergistically reduces tumor growth and metastasis in xenograft models. Altogether, extracellular proteomic rewiring through reduced RTK shedding represents a surprising mechanism for bypass signaling in cancer drug resistance. SIGNIFICANCE Genetic, epigenetic, and gene expression alterations often fail to explain adaptive drug resistance in cancer. This work presents a novel post-translational mechanism of such resistance: Kinase inhibitors, particularly targeting MAPK signaling, increase tumor cell surface receptor levels due to widely reduced proteolysis, allowing tumor signaling to circumvent intended drug action.
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Affiliation(s)
- Miles A Miller
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts. Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Madeleine J Oudin
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Ryan J Sullivan
- Division of Medical Oncology, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Stephanie J Wang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Aaron S Meyer
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts. David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Hyungsoon Im
- Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Dennie T Frederick
- Division of Surgical Oncology, Massachusetts General Hospital, Boston, Massachusetts
| | - Jenny Tadros
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Linda G Griffith
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Hakho Lee
- Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Ralph Weissleder
- Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Keith T Flaherty
- Division of Medical Oncology, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Frank B Gertler
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts. Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Douglas A Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts. David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts. Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts.
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41
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Single cell multiplexed assay for proteolytic activity using droplet microfluidics. Biosens Bioelectron 2016; 81:408-414. [PMID: 26995287 DOI: 10.1016/j.bios.2016.03.002] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Revised: 02/24/2016] [Accepted: 03/02/2016] [Indexed: 11/21/2022]
Abstract
Cellular enzymes interact in a post-translationally regulated fashion to govern individual cell behaviors, yet current platform technologies are limited in their ability to measure multiple enzyme activities simultaneously in single cells. Here, we developed multi-color Förster resonance energy transfer (FRET)-based enzymatic substrates and use them in a microfluidics platform to simultaneously measure multiple specific protease activities from water-in-oil droplets that contain single cells. By integrating the microfluidic platform with a computational analytical method, Proteolytic Activity Matrix Analysis (PrAMA), we are able to infer six different protease activity signals from individual cells in a high throughput manner (~100 cells/experimental run). We characterized protease activity profiles at single cell resolution for several cancer cell lines including breast cancer cell line MDA-MB-231, lung cancer cell line PC-9, and leukemia cell line K-562 using both live-cell and in-situ cell lysis assay formats, with special focus on metalloproteinases important in metastasis. The ability to measure multiple proteases secreted from or expressed in individual cells allows us to characterize cell heterogeneity and has potential applications including systems biology, pharmacology, cancer diagnosis and stem cell biology.
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42
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Facey A, Pinar I, Arthur JF, Qiao J, Jing J, Mado B, Carberry J, Andrews RK, Gardiner EE. A-Disintegrin-And-Metalloproteinase (ADAM) 10 Activity on Resting and Activated Platelets. Biochemistry 2016; 55:1187-94. [DOI: 10.1021/acs.biochem.5b01102] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Adam Facey
- Australian
Centre for Blood Diseases, Monash University, Melbourne, Victoria, Australia 3004
| | - Isaac Pinar
- Department
of Mechanical and Aerospace Engineering, Monash University, Clayton, Victoria, Australia 3168
| | - Jane F. Arthur
- Australian
Centre for Blood Diseases, Monash University, Melbourne, Victoria, Australia 3004
| | - Jianlin Qiao
- Australian
Centre for Blood Diseases, Monash University, Melbourne, Victoria, Australia 3004
| | - Jing Jing
- Australian
Centre for Blood Diseases, Monash University, Melbourne, Victoria, Australia 3004
| | - Belden Mado
- Australian
Centre for Blood Diseases, Monash University, Melbourne, Victoria, Australia 3004
| | - Josie Carberry
- Department
of Mechanical and Aerospace Engineering, Monash University, Clayton, Victoria, Australia 3168
| | - Robert K. Andrews
- Australian
Centre for Blood Diseases, Monash University, Melbourne, Victoria, Australia 3004
| | - Elizabeth E. Gardiner
- Australian
Centre for Blood Diseases, Monash University, Melbourne, Victoria, Australia 3004
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43
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Landry BD, Clarke DC, Lee MJ. Studying Cellular Signal Transduction with OMIC Technologies. J Mol Biol 2015; 427:3416-40. [PMID: 26244521 PMCID: PMC4818567 DOI: 10.1016/j.jmb.2015.07.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Revised: 07/25/2015] [Accepted: 07/27/2015] [Indexed: 11/24/2022]
Abstract
In the gulf between genotype and phenotype exists proteins and, in particular, protein signal transduction systems. These systems use a relatively limited parts list to respond to a much longer list of extracellular, environmental, and/or mechanical cues with rapidity and specificity. Most signaling networks function in a highly non-linear and often contextual manner. Furthermore, these processes occur dynamically across space and time. Because of these complexities, systems and "OMIC" approaches are essential for the study of signal transduction. One challenge in using OMIC-scale approaches to study signaling is that the "signal" can take different forms in different situations. Signals are encoded in diverse ways such as protein-protein interactions, enzyme activities, localizations, or post-translational modifications to proteins. Furthermore, in some cases, signals may be encoded only in the dynamics, duration, or rates of change of these features. Accordingly, systems-level analyses of signaling may need to integrate multiple experimental and/or computational approaches. As the field has progressed, the non-triviality of integrating experimental and computational analyses has become apparent. Successful use of OMIC methods to study signaling will require the "right" experiments and the "right" modeling approaches, and it is critical to consider both in the design phase of the project. In this review, we discuss common OMIC and modeling approaches for studying signaling, emphasizing the philosophical and practical considerations for effectively merging these two types of approaches to maximize the probability of obtaining reliable and novel insights into signaling biology.
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Affiliation(s)
- Benjamin D Landry
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - David C Clarke
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, V5A 1S6 Canada
| | - Michael J Lee
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA; Program in Molecular Medicine, Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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44
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Targeting autocrine HB-EGF signaling with specific ADAM12 inhibition using recombinant ADAM12 prodomain. Sci Rep 2015; 5:15150. [PMID: 26477568 PMCID: PMC4609913 DOI: 10.1038/srep15150] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 09/07/2015] [Indexed: 12/17/2022] Open
Abstract
Dysregulation of ErbB-family signaling underlies numerous pathologies and has been therapeutically targeted through inhibiting ErbB-receptors themselves or their cognate ligands. For the latter, “decoy” antibodies have been developed to sequester ligands including heparin-binding epidermal growth factor (HB-EGF); however, demonstrating sufficient efficacy has been difficult. Here, we hypothesized that this strategy depends on properties such as ligand-receptor binding affinity, which varies widely across the known ErbB-family ligands. Guided by computational modeling, we found that high-affinity ligands such as HB-EGF are more difficult to target with decoy antibodies compared to low-affinity ligands such as amphiregulin (AREG). To address this issue, we developed an alternative method for inhibiting HB-EGF activity by targeting its cleavage from the cell surface. In a model of the invasive disease endometriosis, we identified A Disintegrin and Metalloproteinase 12 (ADAM12) as a protease implicated in HB-EGF shedding. We designed a specific inhibitor of ADAM12 based on its recombinant prodomain (PA12), which selectively inhibits ADAM12 but not ADAM10 or ADAM17. In endometriotic cells, PA12 significantly reduced HB-EGF shedding and resultant cellular migration. Overall, specific inhibition of ligand shedding represents a possible alternative to decoy antibodies, especially for ligands such as HB-EGF that exhibit high binding affinity and localized signaling.
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Moss ML, Koller G, Bartsch JW, Rakow S, Schlomann U, Rasmussen FH. A colorimetric-based amplification system for proteinases including MMP2 and ADAM8. Anal Biochem 2015; 484:75-81. [DOI: 10.1016/j.ab.2015.05.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 05/01/2015] [Accepted: 05/18/2015] [Indexed: 11/25/2022]
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Abstract
The vascular network carries blood throughout the body, delivering oxygen to tissues and providing a pathway for communication between distant organs. The network is hierarchical and structured, but also dynamic, especially at the smaller scales. Remodeling of the microvasculature occurs in response to local changes in oxygen, gene expression, cell-cell communication, and chemical and mechanical stimuli from the microenvironment. These local changes occur as a result of physiological processes such as growth and exercise, as well as acute and chronic diseases including stroke, cancer, and diabetes, and pharmacological intervention. While the vasculature is an important therapeutic target in many diseases, drugs designed to inhibit vascular growth have achieved only limited success, and no drug has yet been approved to promote therapeutic vascular remodeling. This highlights the challenges involved in identifying appropriate therapeutic targets in a system as complex as the vasculature. Systems biology approaches provide a means to bridge current understanding of the vascular system, from detailed signaling dynamics measured in vitro and pre-clinical animal models of vascular disease, to a more complete picture of vascular regulation in vivo. This will translate to an improved ability to identify multi-component biomarkers for diagnosis, prognosis, and monitoring of therapy that are easy to measure in vivo, as well as better drug targets for specific disease states. In this review, we summarize systems biology approaches that have advanced our understanding of vascular function and dysfunction in vivo, with a focus on computational modeling.
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Affiliation(s)
- Lindsay E Clegg
- Institute for Computational Medicine and Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
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Wu L, Claas AM, Sarkar A, Lauffenburger DA, Han J. High-throughput protease activity cytometry reveals dose-dependent heterogeneity in PMA-mediated ADAM17 activation. Integr Biol (Camb) 2015; 7:513-24. [PMID: 25832727 PMCID: PMC4428935 DOI: 10.1039/c5ib00019j] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
As key components of autocrine signaling, pericellular proteases, a disintegrin and metalloproteinases (ADAMs) in particular, are known to impact the microenvironment of individual cells and have significant implications in various pathological situations including cancer, inflammatory and vascular diseases. There is great incentive to develop a high-throughput platform for single-cell measurement of pericellular protease activity, as it is essential for studying the heterogeneity of protease response and the corresponding cell behavioral consequences. In this work, we developed a microfluidic platform to simultaneously monitor protease activity of many single cells in a time-dependent manner. This platform isolates individual microwells rapidly on demand and thus allows single-cell activity measurement of both cell-surface and secreted proteases by confining individual cells with diffusive FRET-based substrates. With this platform, we observed dose-dependent heterogeneous protease activation of HepG2 cells treated with phorbol 12-myristate 13-acetate (PMA). To study the temporal behavior of PMA-induced protease response, we monitored the pericellular protease activity of the same single cells during three different time periods and revealed the diversity in the dynamic patterns of single-cell protease activity profile upon PMA stimulation. The unique temporal information of single-cell protease response can help unveil the complicated functional role of pericellular proteases.
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Affiliation(s)
- Lidan Wu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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Ng EX, Miller MA, Jing T, Lauffenburger DA, Chen CH. Low-volume multiplexed proteolytic activity assay and inhibitor analysis through a pico-injector array. LAB ON A CHIP 2015; 15:1153-1159. [PMID: 25553996 DOI: 10.1039/c4lc01162g] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Secreted active proteases, from families of enzymes such as matrix metalloproteinases (MMPs) and ADAMs (a disintegrin and metalloproteinases), participate in diverse pathological processes. To simultaneously measure multiple specific protease activities, a series of parallel enzyme reactions combined with a series of inhibitor analyses for proteolytic activity matrix analysis (PrAMA) are essential but limited due to the sample quantity requirements and the complexity of performing multiple reactions. To address these issues, we developed a pico-injector array to generate 72 different reactions in picoliter-volume droplets by controlling the sequence of combinational injections, which allowed simultaneous recording of a wide range of multiple enzyme reactions and measurement of inhibitor effects using small sample volumes (~10 μL). Multiple MMP activities were simultaneously determined by 9 different substrates and 2 inhibitors using injections from a pico-injector array. Due to the advantages of inhibitor analysis, the MMP/ADAM activities of MDA-MB-231, a breast cancer cell line, were characterized with high MMP-2, MMP-3 and ADAM-10 activity. This platform could be customized for a wide range of applications that also require multiple reactions with inhibitor analysis to enhance the sensitivity by encapsulating different chemical sensors.
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Affiliation(s)
- Ee Xien Ng
- Department of Biomedical Engineering, National University of Singapore, 9 Engineering Drive 1, Singapore 117575, Singapore.
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Rane T, Zec HC, Wang TH. A barcode-free combinatorial screening platform for matrix metalloproteinase screening. Anal Chem 2015; 87:1950-6. [PMID: 25543856 PMCID: PMC4318618 DOI: 10.1021/ac504330x] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2014] [Accepted: 12/28/2014] [Indexed: 11/30/2022]
Abstract
Application of droplet microfluidics to combinatorial screening applications remains elusive because of the need for composition-identifying unique barcodes. Here we propose a barcode-free continuous flow droplet microfluidic platform to suit the requirements of combinatorial screening applications. We demonstrate robust and repeatable functioning of this platform with matrix metalloproteinase activity screening as a sample application.
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Affiliation(s)
- Tushar
D. Rane
- Department of Biomedical Engineering and Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Helena C. Zec
- Department of Biomedical Engineering and Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Tza-Huei Wang
- Department of Biomedical Engineering and Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
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Abstract
Pancreatic ductal adenocarcinoma (PDAC) has a grim prognosis with less than 5% survivors after 5 years. High expression levels of ADAM8, a metalloprotease-disintegrin, are correlated with poor clinical outcome. We show that ADAM8 expression is associated with increased migration and invasiveness of PDAC cells caused by activation of ERK 1/2 and higher MMP activities. For biological function, ADAM8 requires multimerisation and associates with β1-integrin on the cell surface. A peptidomimetic ADAM8 inhibitor, BK-1361, designed by structural modelling of the disintegrin domain, prevents ADAM8 multimerisation. In PDAC cells, BK-1361 affects ADAM8 function leading to reduced invasiveness, and less ERK 1/2 and MMP activation. BK-1361 application in mice decreased tumour burden and metastasis of implanted pancreatic tumour cells and provides improved metrics of clinical symptoms and survival in a KrasG12D-driven mouse model of PDAC. Thus, our data integrate ADAM8 in pancreatic cancer signalling and validate ADAM8 as a target for PDAC therapy.
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