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Harrigan J, Jacq X. Monitoring Target Engagement of Deubiquitylating Enzymes Using Activity Probes: Past, Present, and Future. Methods Mol Biol 2016; 1449:395-410. [PMID: 27613052 PMCID: PMC7120244 DOI: 10.1007/978-1-4939-3756-1_26] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
Deubiquitylating enzymes or DUBs are a class of enzymes that selectively remove the polypeptide posttranslational modification ubiquitin from a number of substrates. Approximately 100 DUBs exist in human cells and are involved in key regulatory cellular processes, which drive many disease states, making them attractive therapeutic targets. Several aspects of DUB biology have been studied through genetic knock-out or knock-down, genomic, or proteomic studies. However, investigation of enzyme activation and regulation requires additional tools to monitor cellular and physiological dynamics. A comparison between genetic ablation and dominant-negative target validation with pharmacological inhibition often leads to striking discrepancies. Activity probes have been used to profile classes of enzymes, including DUBs, and allow functional and dynamic properties to be assigned to individual proteins. The ability to directly monitor DUB activity within a native biological system is essential for understanding the physiological and pathological role of individual DUBs. We will discuss the evolution of DUB activity probes, from in vitro assay development to their use in monitoring DUB activity in cells and in animal tissues, as well as recent progress and prospects for assessing DUB inhibition in vivo.
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Affiliation(s)
- Jeanine Harrigan
- MISSION Therapeutics Limited, Moneta, Babraham Research Campus, Cambridge, CB22 3AT, UK
| | - Xavier Jacq
- MISSION Therapeutics Limited, Moneta, Babraham Research Campus, Cambridge, CB22 3AT, UK.
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102
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Abstract
Caspases are proteases that are essential components of apoptotic cell death pathways. There are approximately one dozen apoptotic caspases found in organisms where cells die via apoptosis. These caspases are responsible for initiation or execution of apoptosis through the proteolytic cleavage of specific substrates. These substrates contain specific motifs that are recognized and cleaved by caspases that result in alterations of substrate function that promotes the apoptotic phenotype. Analysis of caspase involvement, much like any other protease, can be followed using peptides corresponding to cleavage motifs of these substrates, which can be used as substrates, inhibitors, or affinity-based probes.Different caspases have different substrates and therefore different motifs are recognized by each different caspase. However, these different caspases have a common amino acid recognition pattern containing an aspartic acid residue at the amino-side of the cleavage site. Therefore, caspase substrates have a certain overlap in the cleavage motif as this aspartic acid is found in almost every one. This means that certain peptide motifs are not exclusively cleaved by one single caspase. This lack of exclusive cleavage has brought the use of these motif-based probes into question and spurred the development of truly caspase-specific motifs. This chapter describes the use of peptide-based probes to measure caspase activity while highlighting the limitations of these reagents.
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Affiliation(s)
- Gavin P McStay
- Department of Life Sciences, New York Institute of Technology, 432 Theobald Science Center, Northern Boulevard, Old Westbury, NY, 11568, USA.
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103
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Chen B, Ge SS, Zhao YC, Chen C, Yang S. Activity-based protein profiling: an efficient approach to study serine hydrolases and their inhibitors in mammals and microbes. RSC Adv 2016. [DOI: 10.1039/c6ra20006k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
This review focuses on the identification of serine hydrolases and their inhibitors in mammals and microbes with activity-based protein profiling (ABPP).
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Affiliation(s)
- Biao Chen
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering
- Key Laboratory of Green Pesticide and Agricultural Bioengineering
- Ministry of Education
- Center for R&D of Fine Chemicals of Guizhou University
- Guiyang
| | - Sha-Sha Ge
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering
- Key Laboratory of Green Pesticide and Agricultural Bioengineering
- Ministry of Education
- Center for R&D of Fine Chemicals of Guizhou University
- Guiyang
| | - Yuan-Chao Zhao
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering
- Key Laboratory of Green Pesticide and Agricultural Bioengineering
- Ministry of Education
- Center for R&D of Fine Chemicals of Guizhou University
- Guiyang
| | - Chong Chen
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering
- Key Laboratory of Green Pesticide and Agricultural Bioengineering
- Ministry of Education
- Center for R&D of Fine Chemicals of Guizhou University
- Guiyang
| | - Song Yang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering
- Key Laboratory of Green Pesticide and Agricultural Bioengineering
- Ministry of Education
- Center for R&D of Fine Chemicals of Guizhou University
- Guiyang
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104
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Lazarides AL, Whitley MJ, Strasfeld DB, Cardona DM, Ferrer JM, Mueller JL, Fu HL, DeWitt SB, Brigman BE, Ramanujam N, Kirsch DG, Eward WC. A Fluorescence-Guided Laser Ablation System for Removal of Residual Cancer in a Mouse Model of Soft Tissue Sarcoma. Am J Cancer Res 2016; 6:155-66. [PMID: 26877775 PMCID: PMC4729765 DOI: 10.7150/thno.13536] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 09/28/2015] [Indexed: 12/22/2022] Open
Abstract
The treatment of soft tissue sarcoma (STS) generally involves tumor excision with a wide margin. Although advances in fluorescence imaging make real-time detection of cancer possible, removal is limited by the precision of the human eye and hand. Here, we describe a novel pulsed Nd:YAG laser ablation system that, when used in conjunction with a previously described molecular imaging system, can identify and ablate cancer in vivo. Mice with primary STS were injected with the protease-activatable probe LUM015 to label tumors. Resected tissues from the mice were then imaged and treated with the laser using the paired fluorescence-imaging/ laser ablation device, generating ablation clefts with sub-millimeter precision and minimal underlying tissue damage. Laser ablation was guided by fluorescence to target tumor tissues, avoiding normal structures. The selective ablation of tumor implants in vivo improved recurrence-free survival after tumor resection in a cohort of 14 mice compared to 12 mice that received no ablative therapy. This prototype system has the potential to be modified so that it can be used during surgery to improve recurrence-free survival in patients with cancer.
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105
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Withana NP, Garland M, Verdoes M, Ofori LO, Segal E, Bogyo M. Labeling of active proteases in fresh-frozen tissues by topical application of quenched activity-based probes. Nat Protoc 2015; 11:184-91. [PMID: 26716706 DOI: 10.1038/nprot.2016.004] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Active enzymes, such as proteases, often serve as valuable biomarkers for various disease pathologies. Therefore, methods to detect specific enzyme activities in biological samples can provide information to guide disease detection and diagnosis and to increase our understanding of the biological roles of specific enzyme targets. In this protocol, we outline methods for the topical application of fluorescently quenched activity-based probes (qABPs) to fresh-frozen tissue samples. This technique enables rapid imaging of enzyme activity at cellular resolution, and it can be combined with antibody labeling for immunodiagnosis. In this method, fresh-frozen tissue sections are fixed, incubated with the probe and imaged using fluorescence microscopy. This provides an advance over classical immunohistochemistry (IHC) in that it is rapid (4-8 h) and inexpensive, and it provides information on enzyme activity. Furthermore, it can be used with any of the growing number of fluorescent ABPs to provide data for more effective disease monitoring and diagnosis.
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Affiliation(s)
- Nimali P Withana
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Megan Garland
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Martijn Verdoes
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Leslie O Ofori
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Ehud Segal
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Matthew Bogyo
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA.,Department of Chemical Systems and Biology, Stanford University School of Medicine, Stanford, California, USA.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
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106
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Nguyen PD, Cong VT, Baek C, Min J. Fabrication of peptide stabilized fluorescent gold nanocluster/graphene oxide nanocomplex and its application in turn-on detection of metalloproteinase-9. Biosens Bioelectron 2015; 89:666-672. [PMID: 26725932 DOI: 10.1016/j.bios.2015.12.031] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Revised: 11/30/2015] [Accepted: 12/14/2015] [Indexed: 01/14/2023]
Abstract
This study introduces the double-ligands stabilizing gold nanoclusters and the fabrication of gold nanocluster/graphene nanocomplex as a "turn-on" fluorescent probe for the detection of cancer-related enzyme matrix metalloproteinase-9. A facile, one-step approach was developed for the synthesis of fluorescent gold nanoclusters using peptides and mercaptoundecanoic acid as co-templating ligands. The peptide was designed to possess a metalloproteinase-9 cleavage site and to act not only as a stabilizer but also as a targeting ligand for the enzyme detection. The prepared gold nanoclusters show an intense red fluorescence with a broad adsorption spectrum. In the presence of the enzyme, due to the excellent quenching properties and the negligible background of graphene oxide, the developed peptide-gold nanocluster/graphene nanocomplex yielded an intense "turn-on" fluorescent response, which strongly correlated with the enzyme concentration. The limit of detection of the nanocomplex was 0.15nM. The sensor was successfully applied for "turn-on" detection of metalloproteinase-9 secreted from human breast adenocarcinoma MCF-7 cells with high sensitivity, selectivity, significant improvement in terms of detection time and simplicity.
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Affiliation(s)
- Phuong-Diem Nguyen
- School of Integrative Engineering, Chung-Ang University, Heukseok-dong, Dongjak-gu, Seoul 156-756, Republic of Korea
| | - Vu Thanh Cong
- School of Integrative Engineering, Chung-Ang University, Heukseok-dong, Dongjak-gu, Seoul 156-756, Republic of Korea
| | - Changyoon Baek
- School of Integrative Engineering, Chung-Ang University, Heukseok-dong, Dongjak-gu, Seoul 156-756, Republic of Korea
| | - Junhong Min
- School of Integrative Engineering, Chung-Ang University, Heukseok-dong, Dongjak-gu, Seoul 156-756, Republic of Korea.
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107
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Hütten M, Geukes M, Misas-Villamil JC, van der Hoorn RAL, Grundler FMW, Siddique S. Activity profiling reveals changes in the diversity and activity of proteins in Arabidopsis roots in response to nematode infection. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2015; 97:36-43. [PMID: 26408809 DOI: 10.1016/j.plaphy.2015.09.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2015] [Revised: 08/27/2015] [Accepted: 09/10/2015] [Indexed: 06/05/2023]
Abstract
Cyst nematodes are obligate, sedentary endoparasites with a highly specialised biology and a huge economic impact in agriculture. Successful parasitism involves morphological and physiological modifications of the host cells which lead to the formation of specialised syncytial feeding structures in roots. The development of the syncytium is aided by a cocktail of nematode effectors that manipulate the host plant activities in a complex network of interactions through post-translational modifications. Traditional transcriptomic and proteomic approaches cannot display this functional proteomic information. Activity-based protein profiling (ABPP) is a powerful technology that can be used to investigate the activity of the proteome through activity-based probes. To better understand the functional proteomics of syncytium, ABPP was conducted on syncytia induced by the beet cyst nematode Heterodera schachtii in Arabidopsis roots. Our results demonstrated that the activity of several enzymes is differentially regulated in the syncytium compared to the control roots. Among those specifically activated in the syncytium are a putative S-formyl-glutathione hydrolase (SFGH), a putative methylesterase (MES) and two unidentified enzymes. In contrast, the activities of vacuolar processing enzymes (VPEs) are specifically suppressed in the syncytium. Competition labelling, quantitative gene expression and T-DNA knock-out mutants were used to further characterise the roles of the differentially regulated enzymes during plant-nematode interaction. In conclusion, our study will open the door to generate a comprehensive and integrated view of the host-pathogen warfare that results in the formation of long-term feeding sites for pathogens.
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Affiliation(s)
- Marion Hütten
- Rheinische Friedrich-Wilhelms-University of Bonn, INRES - Molecular Phytomedicine, Karlrobert-Kreiten-Straße 13, 53115 Bonn, Germany.
| | - Melanie Geukes
- Rheinische Friedrich-Wilhelms-University of Bonn, INRES - Molecular Phytomedicine, Karlrobert-Kreiten-Straße 13, 53115 Bonn, Germany.
| | - Johana C Misas-Villamil
- Plant Chemetics Lab, Max-Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany; Botanical Institute and Cluster of Excellence on Plant Sciences, University of Cologne, 50674 Cologne, Germany.
| | - Renier A L van der Hoorn
- Plant Chemetics Lab, Max-Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany; Plant Chemetics Lab, Department of Plant Sciences, University of Oxford, South Parks Road, OX1 3UB Oxford, UK.
| | - Florian M W Grundler
- Rheinische Friedrich-Wilhelms-University of Bonn, INRES - Molecular Phytomedicine, Karlrobert-Kreiten-Straße 13, 53115 Bonn, Germany.
| | - Shahid Siddique
- Rheinische Friedrich-Wilhelms-University of Bonn, INRES - Molecular Phytomedicine, Karlrobert-Kreiten-Straße 13, 53115 Bonn, Germany.
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108
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Shaulov-Rotem Y, Merquiol E, Weiss-Sadan T, Moshel O, Salpeter S, Shabat D, Kaschani F, Kaiser M, Blum G. A novel quenched fluorescent activity-based probe reveals caspase-3 activity in the endoplasmic reticulum during apoptosis. Chem Sci 2015; 7:1322-1337. [PMID: 29910890 PMCID: PMC5975724 DOI: 10.1039/c5sc03207e] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 11/07/2015] [Indexed: 01/03/2023] Open
Abstract
A selective quenched activity-based probe detects caspase-3 activity in the endoplasmic reticulum of cancerous cells during apoptosis.
The caspases are a family of cysteine proteases that are key regulators of apoptosis and their activity may thus serve as a good marker to monitor cell death. We have developed a quenched fluorescent activity-based probe (qABP) that is selective for caspase-3 activity and emits a fluorescent signal after covalently modifying its target. The probe has a wide range of potential applications, e.g. in real-time imaging, FACS analysis or biochemical quantification of caspase activity in intact cells. Application of the probe allowed us to monitor caspase-3 activation after chemotherapy-treatment and to distinguish between apoptosis sensitive and resistant cells. Moreover, it enabled real-time high-resolution visualization of active caspase-3 during apoptosis. This led to the surprising finding that in cancerous cells active caspase-3 is not only found at the familiar cellular locations but also in mitochondria and the endoplasmic reticulum. Thus, our novel covalent probe allows high spatial and temporal resolution imaging of caspase-3 activation and may thus be used as an effective tool to study molecular mechanisms of programmed cell death in healthy and disease states.
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Affiliation(s)
- Yulia Shaulov-Rotem
- Institute of Drug Research , The School of Pharmacy , The Faculty of Medicine , Campus Ein Karem , The Hebrew University , Jerusalem , 9112001 , Israel
| | - Emmanuelle Merquiol
- Institute of Drug Research , The School of Pharmacy , The Faculty of Medicine , Campus Ein Karem , The Hebrew University , Jerusalem , 9112001 , Israel
| | - Tommy Weiss-Sadan
- Institute of Drug Research , The School of Pharmacy , The Faculty of Medicine , Campus Ein Karem , The Hebrew University , Jerusalem , 9112001 , Israel
| | - Ofra Moshel
- Institute of Drug Research , The School of Pharmacy , The Faculty of Medicine , Campus Ein Karem , The Hebrew University , Jerusalem , 9112001 , Israel
| | - Seth Salpeter
- Institute of Drug Research , The School of Pharmacy , The Faculty of Medicine , Campus Ein Karem , The Hebrew University , Jerusalem , 9112001 , Israel
| | - Doron Shabat
- School of Chemistry , Faculty of Exact Sciences , Tel-Aviv University , Tel Aviv , 69978 , Israel
| | - Farnusch Kaschani
- Department of Chemical Biology , University of Duisburg-Essen , Center for Medical Biotechnology , Faculty of Biology , 45117 Essen , Germany
| | - Markus Kaiser
- Department of Chemical Biology , University of Duisburg-Essen , Center for Medical Biotechnology , Faculty of Biology , 45117 Essen , Germany
| | - Galia Blum
- Institute of Drug Research , The School of Pharmacy , The Faculty of Medicine , Campus Ein Karem , The Hebrew University , Jerusalem , 9112001 , Israel
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109
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Poreba M, Szalek A, Kasperkiewicz P, Rut W, Salvesen GS, Drag M. Small Molecule Active Site Directed Tools for Studying Human Caspases. Chem Rev 2015; 115:12546-629. [PMID: 26551511 DOI: 10.1021/acs.chemrev.5b00434] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Caspases are proteases of clan CD and were described for the first time more than two decades ago. They play critical roles in the control of regulated cell death pathways including apoptosis and inflammation. Due to their involvement in the development of various diseases like cancer, neurodegenerative diseases, or autoimmune disorders, caspases have been intensively investigated as potential drug targets, both in academic and industrial laboratories. This review presents a thorough, deep, and systematic assessment of all technologies developed over the years for the investigation of caspase activity and specificity using substrates and inhibitors, as well as activity based probes, which in recent years have attracted considerable interest due to their usefulness in the investigation of biological functions of this family of enzymes.
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Affiliation(s)
- Marcin Poreba
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Technology , Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Aleksandra Szalek
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Technology , Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Paulina Kasperkiewicz
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Technology , Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Wioletta Rut
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Technology , Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Guy S Salvesen
- Program in Cell Death and Survival Networks, Sanford Burnham Prebys Medical Discovery Institute , La Jolla, California 92037, United States
| | - Marcin Drag
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Technology , Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
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110
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Ji K, Heyza J, Cavallo-Medved D, Sloane BF. Pathomimetic cancer avatars for live-cell imaging of protease activity. Biochimie 2015; 122:68-76. [PMID: 26375517 DOI: 10.1016/j.biochi.2015.09.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 09/10/2015] [Indexed: 12/12/2022]
Abstract
Proteases are essential for normal physiology as well as multiple diseases, e.g., playing a causative role in cancer progression, including in tumor angiogenesis, invasion, and metastasis. Identification of dynamic alterations in protease activity may allow us to detect early stage cancers and to assess the efficacy of anti-cancer therapies. Despite the clinical importance of proteases in cancer progression, their functional roles individually and within the context of complex protease networks have not yet been well defined. These gaps in our understanding might be addressed with: 1) accurate and sensitive tools and methods to directly identify changes in protease activities in live cells, and 2) pathomimetic avatars for cancer that recapitulate in vitro the tumor in the context of its cellular and non-cellular microenvironment. Such avatars should be designed to facilitate mechanistic studies that can be translated to animal models and ultimately the clinic. Here, we will describe basic principles and recent applications of live-cell imaging for identification of active proteases. The avatars optimized by our laboratory are three-dimensional (3D) human breast cancer models in a matrix of reconstituted basement membrane (rBM). They are designated mammary architecture and microenvironment engineering (MAME) models as they have been designed to mimic the structural and functional interactions among cell types in the normal and cancerous human breast. We have demonstrated the usefulness of these pathomimetic avatars for following dynamic and temporal changes in cell:cell interactions and quantifying changes in protease activity associated with these interactions in real-time (4D). We also briefly describe adaptation of the avatars to custom-designed and fabricated tissue architecture and microenvironment engineering (TAME) chambers that enhance our ability to analyze concomitant changes in the malignant phenotype and the associated tumor microenvironment.
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Affiliation(s)
- Kyungmin Ji
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI 48201, USA.
| | - Joshua Heyza
- Cancer Biology Graduate Program, Wayne State University School of Medicine, Detroit, MI 48201, USA; Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, USA.
| | - Dora Cavallo-Medved
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI 48201, USA; Department of Biological Sciences, University of Windsor, Windsor, Canada.
| | - Bonnie F Sloane
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI 48201, USA; Cancer Biology Graduate Program, Wayne State University School of Medicine, Detroit, MI 48201, USA; Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, USA; Department of Biological Sciences, University of Windsor, Windsor, Canada.
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111
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Chagnon F, Bourgouin A, Lebel R, Bonin MA, Marsault E, Lepage M, Lesur O. Smart imaging of acute lung injury: exploration of myeloperoxidase activity using in vivo endoscopic confocal fluorescence microscopy. Am J Physiol Lung Cell Mol Physiol 2015; 309:L543-51. [PMID: 26232301 DOI: 10.1152/ajplung.00289.2014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 07/24/2015] [Indexed: 02/07/2023] Open
Abstract
The pathophysiology of acute lung injury (ALI) is well characterized, but its real-time assessment at bedside remains a challenge. When patients do not improve after 1 wk despite supportive therapies, physicians have to consider open lung biopsy (OLB) to identify the process(es) at play. Sustained inflammation and inadequate repair are often observed in this context. OLB is neither easy to perform in a critical setting nor exempt from complications. Herein, we explore intravital endoscopic confocal fluorescence microscopy (ECFM) of the lung in vivo combined with the use of fluorescent smart probe(s) activated by myeloperoxidase (MPO). MPO is a granular enzyme expressed by polymorphonuclear neutrophils (PMNs) and alveolar macrophages (AMs), catalyzing the synthesis of hypoclorous acid, a by-product of hydrogen peroxide. Activation of these probes was first validated in vitro in relevant cells (i.e., AMs and PMNs) and on MPO-non-expressing cells (as negative controls) and then tested in vivo using three rat models of ALI and real-time intravital imaging with ECFM. Semiquantitative image analyses revealed that in vivo probe-related cellular/background fluorescence was associated with corresponding enhanced lung enzymatic activity and was partly prevented by specific MPO inhibition. Additional ex vivo phenotyping was performed, confirming that fluorescent cells were neutrophil elastase(+) (PMNs) or CD68(+) (AMs). This work is a first step toward "virtual biopsy" of ALI without OLB.
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Affiliation(s)
- Frédéric Chagnon
- Soins Intensifs Médicaux, Département de Médecine; Centre de Recherche Clinique du CHUS
| | - Alexandra Bourgouin
- Centre de Recherche Clinique du CHUS; Centre d'Imagerie Moléculaire de Sherbrooke; and
| | - Réjean Lebel
- Centre de Recherche Clinique du CHUS; Centre d'Imagerie Moléculaire de Sherbrooke; and
| | - Marc-André Bonin
- Centre de Recherche Clinique du CHUS; Laboratoire de Chimie Médicinale, Institut de Pharmacologie de Sherbrooke Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Eric Marsault
- Centre de Recherche Clinique du CHUS; Laboratoire de Chimie Médicinale, Institut de Pharmacologie de Sherbrooke Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Martin Lepage
- Centre de Recherche Clinique du CHUS; Centre d'Imagerie Moléculaire de Sherbrooke; and
| | - Olivier Lesur
- Soins Intensifs Médicaux, Département de Médecine; Centre de Recherche Clinique du CHUS; Centre d'Imagerie Moléculaire de Sherbrooke; and
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112
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Li L, Zhang CW, Ge J, Qian L, Chai BH, Zhu Q, Lee JS, Lim KL, Yao SQ. A Small-Molecule Probe for Selective Profiling and Imaging of Monoamine Oxidase B Activities in Models of Parkinson’s Disease. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201504441] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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113
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Li L, Zhang CW, Ge J, Qian L, Chai BH, Zhu Q, Lee JS, Lim KL, Yao SQ. A Small-Molecule Probe for Selective Profiling and Imaging of Monoamine Oxidase B Activities in Models of Parkinson’s Disease. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/anie.201504441] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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114
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Abstract
Mounting evidence suggests that a more extensive surgical resection is associated with an improved life expectancy for both low-grade and high-grade glioma patients. However, radiographically complete resections are not often achieved in many cases because of the lack of sensitivity and specificity of current neurosurgical guidance techniques at the margins of diffuse infiltrative gliomas. Intraoperative fluorescence imaging offers the potential to improve the extent of resection and to investigate the possible benefits of resecting beyond the radiographic margins. Here, we provide a review of wide-field and high-resolution fluorescence-imaging strategies that are being developed for neurosurgical guidance, with a focus on emerging imaging technologies and clinically viable contrast agents. The strengths and weaknesses of these approaches will be discussed, as well as issues that are being addressed to translate these technologies into the standard of care.
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Affiliation(s)
- Jonathan T C Liu
- *Department of Biomedical Engineering, Stony Brook University, Stony Brook, New York; ‡Barrow Brain Tumor Research Center, Division of Neurosurgical Oncology, Barrow Neurological Institute, St. Joseph's Hospital and Medical Center, Phoenix, Arizona
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115
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Medina-Cleghorn D, Nomura DK. Exploring metabolic pathways and regulation through functional chemoproteomic and metabolomic platforms. ACTA ACUST UNITED AC 2015; 21:1171-84. [PMID: 25237861 DOI: 10.1016/j.chembiol.2014.07.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2014] [Revised: 07/15/2014] [Accepted: 07/21/2014] [Indexed: 02/07/2023]
Abstract
Genome sequencing efforts have revealed a strikingly large number of uncharacterized genes, including poorly or uncharacterized metabolic enzymes, metabolites, and metabolic networks that operate in normal physiology, and those enzymes and pathways that may be rewired under pathological conditions. Although deciphering the functions of the uncharacterized metabolic genome is a challenging prospect, it also presents an opportunity for identifying novel metabolic nodes that may be important in disease therapy. In this review, we will discuss the chemoproteomic and metabolomic platforms used in identifying, characterizing, and targeting nodal metabolic pathways important in physiology and disease, describing an integrated workflow for functional mapping of metabolic enzymes.
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Affiliation(s)
- Daniel Medina-Cleghorn
- Program in Metabolic Biology and Molecular Toxicology, Department of Nutritional Sciences and Toxicology, 127 Morgan Hall, Berkeley, CA 94720, USA
| | - Daniel K Nomura
- Program in Metabolic Biology and Molecular Toxicology, Department of Nutritional Sciences and Toxicology, 127 Morgan Hall, Berkeley, CA 94720, USA.
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116
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Detection of protease activity in cells and animals. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1864:130-42. [PMID: 25960278 DOI: 10.1016/j.bbapap.2015.04.029] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 04/21/2015] [Accepted: 04/28/2015] [Indexed: 01/05/2023]
Abstract
Proteases are involved in a wide variety of biologically and medically important events. They are entangled in a complex network of processes that regulate their activity, which makes their study intriguing, but challenging. For comprehensive understanding of protease biology and effective drug discovery, it is therefore essential to study proteases in models that are close to their complex native environments such as live cells or whole organisms. Protease activity can be detected by reporter substrates and activity-based probes, but not all of these reagents are suitable for intracellular or in vivo use. This review focuses on the detection of proteases in cells and in vivo. We summarize the use of probes and substrates as molecular tools, discuss strategies to deliver these tools inside cells, and describe sophisticated read-out techniques such as mass spectrometry and various imaging applications. This article is part of a Special Issue entitled: Physiological Enzymology and Protein Functions.
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117
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Design of a functional cyclic HSV1-TK reporter and its application to PET imaging of apoptosis. Nat Protoc 2015; 10:807-21. [PMID: 25927390 DOI: 10.1038/nprot.2015.048] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Positron emission tomography (PET) is a sensitive and noninvasive imaging method that is widely used to explore molecular events in living subjects. PET can precisely and quantitatively evaluate cellular apoptosis, which has a crucial role in various physiological and pathological processes. In this protocol, we describe the design and use of an engineered cyclic herpes simplex virus 1-thymidine kinase (HSV1-TK) PET reporter whose kinase activity is specifically switched on by apoptosis. The expression of cyclic TK (cTK) in healthy cells leads to inactive product, whereas the activation of apoptosis through the caspase-3 pathway cleaves cTK, thus restoring its activity and enabling PET imaging. In addition to detailing the design and construction of the cTK plasmid in this protocol, we include assays for evaluating the function and specificity of the cTK reporter in apoptotic cells, such as assays for measuring the cell uptake of PET tracer in apoptotic cells, correlating doxorubicin (Dox)-induced cell apoptosis to cTK function recovery, and in vivo PET imaging of cancer cell apoptosis, and we also include corresponding data acquisition methods. The time to build the entire cTK reporter is ∼2-3 weeks. The selection of a stable cancer cell line takes ∼4-6 weeks. The time to implement assays regarding cTK function in apoptotic cells and the in vivo imaging varies depending on the experiment. The cyclization strategy described in this protocol can also be adapted to create other reporter systems for broad biomedical applications.
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118
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119
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Edgington LE, Bogyo M. In vivo imaging and biochemical characterization of protease function using fluorescent activity-based probes. ACTA ACUST UNITED AC 2015; 5:25-44. [PMID: 23788323 DOI: 10.1002/9780470559277.ch120235] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Activity-based probes (ABPs) are reactive small molecules that covalently bind to active enzymes. When tagged with a fluorophore, ABPs serve as powerful tools to investigate enzymatic activity across a wide variety of applications. In this article, detailed protocols are provided for using fluorescent ABPs to biochemically characterize the activity of proteases in vitro. Furthermore, descriptions are provided of how these probes can be applied to image protease activity in live animals and tissues along with subsequent analysis by histology, flow cytometry, and SDS-PAGE.
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Affiliation(s)
- Laura E Edgington
- Cancer Biology Program, Stanford University School of Medicine, Stanford, California, USA
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120
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Takaoka Y, Nishikawa Y, Hashimoto Y, Sasaki K, Hamachi I. Ligand-directed dibromophenyl benzoate chemistry for rapid and selective acylation of intracellular natural proteins. Chem Sci 2015; 6:3217-3224. [PMID: 28706692 PMCID: PMC5490417 DOI: 10.1039/c5sc00190k] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Accepted: 03/20/2015] [Indexed: 12/28/2022] Open
Abstract
A rapid and selective protein labeling method, LDBB chemistry is a useful tool for natural protein imaging in living cells.
A rapid and selective ligand-directed chemical reaction was developed for the acylation of proteins in living cells on the basis of ligand-directed chemistry. By fine tuning the reactivity and stability of the phenyl ester derivatives, we successfully identified ortho-dibromophenyl benzoate as the optimal reactive motif. It was sufficiently stable in an aqueous buffer, hydrolyzing less than 10% after 13 h of incubation, but reactive enough for efficient and selective protein labeling in living mammalian cells, as well as in vitro (referred to as ligand-directed dibromophenyl benzoate (LDBB) chemistry). Using this chemistry, various fluorophores can be tethered to the target protein directly, which allows fluorescence visualization of the labeled protein in live cells using different colored fluorophore groups (including coumarin, fluorescein and rhodamine). Furthermore, this labeling is applicable to not only an overexpressed protein (E. coli dihydrofolate reductase) but also endogenous human carbonic anhydrase II and XII under living cell conditions. LDBB chemistry is a new entry of ligand-directed protein labeling methods, and should be particularly useful for the imaging of natural proteins in living cells.
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Affiliation(s)
- Yousuke Takaoka
- Department of Synthetic Chemistry and Biological Chemistry , Graduate School of Engineering Kyoto University , Katsura , Kyoto 615-8510 , Japan . ; ; Tel: +81-22-795-6557
| | - Yuki Nishikawa
- Department of Synthetic Chemistry and Biological Chemistry , Graduate School of Engineering Kyoto University , Katsura , Kyoto 615-8510 , Japan . ; ; Tel: +81-22-795-6557
| | - Yuki Hashimoto
- Department of Synthetic Chemistry and Biological Chemistry , Graduate School of Engineering Kyoto University , Katsura , Kyoto 615-8510 , Japan . ; ; Tel: +81-22-795-6557
| | - Kenta Sasaki
- Department of Synthetic Chemistry and Biological Chemistry , Graduate School of Engineering Kyoto University , Katsura , Kyoto 615-8510 , Japan . ; ; Tel: +81-22-795-6557
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry , Graduate School of Engineering Kyoto University , Katsura , Kyoto 615-8510 , Japan . ; ; Tel: +81-22-795-6557.,Core Research for Evolutional Science and Technology (CREST) , Japan Science and Technology Agency , 5 Sanbancho , Chiyoda-ku , Tokyo 102-0075 , Japan
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121
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Song Z, Takaoka Y, Kioi Y, Komatsu K, Tamura T, Miki T, Hamachi I. Extended Affinity-guided DMAP Chemistry with a Finely Tuned Acyl Donor for Intracellular FKBP12 Labeling. CHEM LETT 2015. [DOI: 10.1246/cl.141065] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Zhining Song
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University
| | - Yousuke Takaoka
- Department of Chemistry, Graduate School of Science, Tohoku University
| | - Yoshiyuki Kioi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University
| | - Kazuhiro Komatsu
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University
| | - Tomonori Tamura
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University
| | - Takayuki Miki
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University
- Japan Science and Technology Agency (JST), CREST
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122
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Nejadnik H, Ye D, Lenkov OD, Donig J, Martin JE, Castillo R, Derugin N, Sennino B, Rao J, Daldrup-Link HE. Magnetic resonance imaging of stem cell apoptosis in arthritic joints with a caspase activatable contrast agent. ACS NANO 2015; 9:1150-60. [PMID: 25597243 PMCID: PMC4441518 DOI: 10.1021/nn504494c] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
About 43 million individuals in the U.S. encounter cartilage injuries due to trauma or osteoarthritis, leading to joint pain and functional disability. Matrix-associated stem cell implants (MASI) represent a promising approach for repair of cartilage defects. However, limited survival of MASI creates a significant bottleneck for successful cartilage regeneration outcomes and functional reconstitution. We report an approach for noninvasive detection of stem cell apoptosis with magnetic resonance imaging (MRI), based on a caspase-3-sensitive nanoaggregation MRI probe (C-SNAM). C-SNAM self-assembles into nanoparticles after hydrolysis by caspase-3, leading to 90% amplification of (1)H MR signal and prolonged in vivo retention. Following intra-articular injection, C-SNAM causes significant MR signal enhancement in apoptotic MASI compared to viable MASI. Our results indicate that C-SNAM functions as an imaging probe for stem cell apoptosis in MASI. This concept could be applied to a broad range of cell transplants and target sites.
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Affiliation(s)
- Hossein Nejadnik
- Department of Radiology and Molecular Imaging Program at Stanford (MIPS), Stanford School of Medicine, Stanford, CA
| | - Deju Ye
- Department of Radiology and Molecular Imaging Program at Stanford (MIPS), Stanford School of Medicine, Stanford, CA
| | - Olga D. Lenkov
- Department of Radiology and Molecular Imaging Program at Stanford (MIPS), Stanford School of Medicine, Stanford, CA
| | - Jessica Donig
- Department of Radiology and Molecular Imaging Program at Stanford (MIPS), Stanford School of Medicine, Stanford, CA
| | - John E. Martin
- Department of Radiology and Molecular Imaging Program at Stanford (MIPS), Stanford School of Medicine, Stanford, CA
| | - Rostislav Castillo
- Department of Radiology and Molecular Imaging Program at Stanford (MIPS), Stanford School of Medicine, Stanford, CA
| | - Nikita Derugin
- Department of Radiology and Molecular Imaging Program at Stanford (MIPS), Stanford School of Medicine, Stanford, CA
| | - Barbara Sennino
- Comprehensive Cancer Center, Cardiovascular Research Institute and Department of Anatomy, University of California San Francisco, San Francisco, CA
| | - Jianghong Rao
- Department of Radiology and Molecular Imaging Program at Stanford (MIPS), Stanford School of Medicine, Stanford, CA
| | - Heike E. Daldrup-Link
- Department of Radiology and Molecular Imaging Program at Stanford (MIPS), Stanford School of Medicine, Stanford, CA
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123
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Abstract
Eukaryotic and prokaryotic organisms possess huge numbers of uncharacterized enzymes. Selective inhibitors offer powerful probes for assigning functions to enzymes in native biological systems. Here, we discuss how the chemical proteomic platform activity-based protein profiling (ABPP) can be implemented to discover selective and in vivo-active inhibitors for enzymes. We further describe how these inhibitors have been used to delineate the biochemical and cellular functions of enzymes, leading to the discovery of metabolic and signaling pathways that make important contributions to human physiology and disease. These studies demonstrate the value of selective chemical probes as drivers of biological inquiry.
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Affiliation(s)
- Micah J Niphakis
- The Skaggs Institute for Chemical Biology and the Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037;
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124
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Serim S, Baer P, Verhelst SHL. Mixed alkyl aryl phosphonate esters as quenched fluorescent activity-based probes for serine proteases. Org Biomol Chem 2015; 13:2293-9. [DOI: 10.1039/c4ob02444c] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The synthesis of quenched fluorescent activity-based probes for serine proteases based on a phosphonate reactive group is reported.
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Affiliation(s)
- Sevnur Serim
- Lehrstuhl für Chemie der Biopolymere
- Technische Universität München
- 85354 Freising
- Germany
| | - Philipp Baer
- Lehrstuhl für Chemie der Biopolymere
- Technische Universität München
- 85354 Freising
- Germany
| | - Steven H. L. Verhelst
- Lehrstuhl für Chemie der Biopolymere
- Technische Universität München
- 85354 Freising
- Germany
- Leibniz Institute for Analytical Sciences
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125
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Tavakoli S, Vashist A, Sadeghi MM. Molecular imaging of plaque vulnerability. J Nucl Cardiol 2014; 21:1112-28; quiz 1129. [PMID: 25124827 PMCID: PMC4229449 DOI: 10.1007/s12350-014-9959-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 07/08/2014] [Indexed: 01/24/2023]
Abstract
Over the past decade, significant progress has been made in the development of novel imaging strategies focusing on the biology of the vessel wall for identification of vulnerable plaques. While the majority of these studies are still in the pre-clinical stage, few techniques (e.g., (18)F-FDG and (18)F-NaF PET imaging) have already been evaluated in clinical studies with promising results. Here, we will briefly review the pathobiology of atherosclerosis and discuss molecular imaging strategies that have been developed to target these events, with an emphasis on mechanisms that are associated with atherosclerotic plaque vulnerability.
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Affiliation(s)
- Sina Tavakoli
- Department of Radiology, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Aseem Vashist
- Section of Cardiology, University of Connecticut School of Medicine, Farmington, CT, United States
- VA Connecticut Healthcare System, West Haven, CT, United States
| | - Mehran M. Sadeghi
- Section of Cardiovascular Medicine and Cardiovascular Research Center, Yale University School of Medicine, New Haven, CT, United States
- VA Connecticut Healthcare System, West Haven, CT, United States
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126
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Lee SK, Mortensen LJ, Lin CP, Tung CH. An authentic imaging probe to track cell fate from beginning to end. Nat Commun 2014; 5:5216. [PMID: 25323442 PMCID: PMC4852472 DOI: 10.1038/ncomms6216] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 09/09/2014] [Indexed: 12/18/2022] Open
Abstract
Accurate tracing of cell viability is critical for optimizing delivery methods and evaluating the efficacy and safety of cell therapeutics. A nanoparticle-based cell tracker is developed to image cell fate from live to dead. The particle is fabricated from two types of optically quenched polyelectrolytes, a life indicator and a death indicator, through electrostatic interactions. On incubation with cells, the fabricated bifunctional nanoprobes are taken up efficiently and the first colour is produced by normal intracellular proteolysis, reflecting the healthy status of the cells. Depending on the number of coated layers, the signal can persist for several replication cycles. However, as the cells begin dying, the second colour appears quickly to reflect the new cell status. Using this chameleon-like cell tracker, live cells can be distinguished from apoptotic and necrotic cells instantly and definitively.
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Affiliation(s)
- Seung Koo Lee
- Molecular Imaging Innovations Institute, Department of Radiology, Weill Cornell Medical College, 413 East 69th Street, Box 290, New York, New York 10021, USA
| | - Luke J Mortensen
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Charles P Lin
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Ching-Hsuan Tung
- Molecular Imaging Innovations Institute, Department of Radiology, Weill Cornell Medical College, 413 East 69th Street, Box 290, New York, New York 10021, USA
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127
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Vickers CJ, González-Páez GE, Wolan DW. Discovery of a highly selective caspase-3 substrate for imaging live cells. ACS Chem Biol 2014; 9:2199-203. [PMID: 25133295 DOI: 10.1021/cb500586p] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Caspases are a family of cysteine proteases that are well-known for their roles in apoptosis and inflammation. Recent studies provide evidence that caspases are also integral to many additional cellular processes, such as differentiation and proliferation. Likewise, aberrant caspase activity has been implicated in the progression of several diseases, including neurodegenerative disorders, cancer, cardiovascular disease, and sepsis. These observations establish the importance of caspases to a diverse array of physiological functions and future endeavors will undoubtedly continue to elucidate additional processes that require caspase activity. Unfortunately, the existence of 11 functional human caspases, with overlapping substrate specificities, confounds the ability to confidently assign one or more isoforms to biological phenomena. Herein, we characterize a first-in-class FRET substrate that is selectively recognized by active caspase-3 over other initiator and executioner caspases. We further apply this substrate to specifically image caspase-3 activity in live cells undergoing apoptosis.
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Affiliation(s)
- Chris J. Vickers
- Departments of Molecular
and Experimental Medicine and Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Gonzalo E. González-Páez
- Departments of Molecular
and Experimental Medicine and Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Dennis W. Wolan
- Departments of Molecular
and Experimental Medicine and Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, United States
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128
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Zhao Y, Marjanovic M, Chaney EJ, Graf BW, Mahmassani Z, Boppart MD, Boppart SA. Longitudinal label-free tracking of cell death dynamics in living engineered human skin tissue with a multimodal microscope. BIOMEDICAL OPTICS EXPRESS 2014; 5:3699-716. [PMID: 25360383 PMCID: PMC4206335 DOI: 10.1364/boe.5.003699] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 09/03/2014] [Accepted: 09/06/2014] [Indexed: 05/04/2023]
Abstract
We demonstrate real-time, longitudinal, label-free tracking of apoptotic and necrotic cells in living tissue using a multimodal microscope. The integrated imaging platform combines multi-photon microscopy (MPM, based on two-photon excitation fluorescence), optical coherence microscopy (OCM), and fluorescence lifetime imaging microscopy (FLIM). Three-dimensional (3-D) co-registered images are captured that carry comprehensive information of the sample, including structural, molecular, and metabolic properties, based on light scattering, autofluorescence intensity, and autofluorescence lifetime, respectively. Different cell death processes, namely, apoptosis and necrosis, of keratinocytes from different epidermal layers are longitudinally monitored and investigated. Differentiation of the two cell death processes in a complex living tissue environment is enabled by quantitative image analysis and high-confidence classification processing based on the multidimensional, cross-validating imaging data. These results suggest that despite the limitations of each individual label-free modality, this multimodal imaging approach holds the promise for studies of different cell death processes in living tissue and in vivo organs.
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Affiliation(s)
- Youbo Zhao
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Marina Marjanovic
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Eric J. Chaney
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Benedikt W. Graf
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Ziad Mahmassani
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Kinesiology and Community Health, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Marni D. Boppart
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Kinesiology and Community Health, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Stephen A. Boppart
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Internal Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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129
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McStay GP, Green DR. Identification of active caspases using affinity-based probes. Cold Spring Harb Protoc 2014; 2014:856-60. [PMID: 25086016 DOI: 10.1101/pdb.prot080309] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Small-molecule inhibitors of caspases can be modified with moieties such as biotin or fluorescent molecules. After the inhibitor molecule has bound to an active caspase, the caspase itself becomes labeled and can be isolated using affinity purification. This protocol describes the use of the biotinylated pan-caspase inhibitor VAD-FMK and streptavidin beads to isolate active caspases. These caspases are then separated by gel electrophoresis and identified with caspase-specific antibodies using western blotting techniques. Other caspase inhibitors bound with biotin or other labels can be substituted in this assay; labeled inhibitors are available commercially as either pan-caspase or caspase-specific probes.
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Affiliation(s)
- Gavin P McStay
- Department of Life Sciences, New York Institute of Technology, Old Westbury, New York 11568
| | - Douglas R Green
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105
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130
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McStay GP, Green DR. Measuring apoptosis: caspase inhibitors and activity assays. Cold Spring Harb Protoc 2014; 2014:799-806. [PMID: 25086023 DOI: 10.1101/pdb.top070359] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Caspases are proteases that initiate and execute apoptotic cell death. These caspase-dependent events are caused by cleavage of specific substrates that propagate the proapoptotic signal. A number of techniques have been developed to follow caspase activity in vitro and from apoptotic cellular extracts. Many of these techniques use molecules that are based on optimal peptide motifs for each caspase and on our understanding of caspase cleavage events that occur during apoptosis. Although these approaches are useful, there are several drawbacks associated with them. The optimal peptide motifs are not unique recognition sites for each caspase, so techniques that use them may yield information about more than one caspase. Furthermore, caspase cleavage does not take into account the different caspase activation mechanisms. Recently, probes having greater specificity for individual caspases have been developed and are being used successfully. This introduction provides background on the various caspases and introduces a set of complementary techniques to examine the activity, substrate specificity, and activation status of caspases from in vitro or cell culture experiments.
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Affiliation(s)
- Gavin P McStay
- Department of Life Sciences, New York Institute of Technology, Old Westbury, New York 11568
| | - Douglas R Green
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105
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131
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Li Z, Wang D, Li L, Pan S, Na Z, Tan CYJ, Yao SQ. "Minimalist" cyclopropene-containing photo-cross-linkers suitable for live-cell imaging and affinity-based protein labeling. J Am Chem Soc 2014; 136:9990-8. [PMID: 24972113 DOI: 10.1021/ja502780z] [Citation(s) in RCA: 144] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Target identification of bioactive compounds within the native cellular environment is important in biomedical research and drug discovery, but it has traditionally been carried out in vitro. Information about how such molecules interact with their endogenous targets (on and off) is currently highly limited. An ideal strategy would be one that recapitulates protein-small molecule interactions in situ (e.g., in living cells) and at the same time enables enrichment of these complexes for subsequent proteome-wide target identification. Similarly, small molecule-based imaging approaches are becoming increasingly available for in situ monitoring of a variety of proteins including enzymes. Chemical proteomic strategies for simultaneous bioimaging and target identification of noncovalent bioactive compounds in live mammalian cells, however, are currently not available. This is due to a lack of photoaffinity labels that are minimally modified from their parental compounds, yet chemically tractable using copper-free bioorthogonal chemistry. We have herein developed novel minimalist linkers containing both an alkyl diazirine and a cyclopropene. We have shown chemical probes (e.g., BD-2) made from such linkers could be used for simultaneous in situ imaging and covalent labeling of endogenous BRD-4 (an important epigenetic protein) via a rapid, copper-free, tetrazine-cyclopropene ligation reaction (k2 > 5 M(-1) s(-1)). The key features of our cyclopropenes, with their unique C-1 linkage to BRD-4-targeting moiety, are their tunable reactivity and solubility, relative stability, and synthetic accessibility. BD-2, which is a linker-modified analogue of (+)-JQ1 (a recently discovered nanomolar protein-protein-interaction inhibitor of BRD-4), was subsequently used in a cell-based proteome profiling experiment for large-scale identification of potential off-targets of (+)-JQ1. Several newly identified targets were subsequently confirmed by preliminary validation experiments.
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Affiliation(s)
- Zhengqiu Li
- Department of Chemistry, National University of Singapore , 3 Science Drive 3, Singapore 117543
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132
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Willems LI, Overkleeft HS, van Kasteren SI. Current developments in activity-based protein profiling. Bioconjug Chem 2014; 25:1181-91. [PMID: 24946272 DOI: 10.1021/bc500208y] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Activity-based protein profiling (ABPP) has emerged as a powerful strategy to study the activity of enzymes in complex proteomes. The aim of ABPP is to selectively visualize only the active forms of particular enzymes using chemical probes termed activity-based probes (ABPs). These probes are directed to the active site of a particular target protein (or protein family) where they react in a mechanism-based manner with an active site residue. This results in the selective labeling of only the catalytically active form of the enzyme, usually in a covalent manner. Besides the monitoring of a specific enzymatic activity, ABPP strategies have also been used to identify and characterize (unknown) protein functions, to study up- and down-regulation of enzymatic activity in various disease states, to discover and evaluate putative new enzyme inhibitors, and to identify the protein targets of covalently binding natural products. In this Topical Review we will provide a brief overview of some of the recent developments in the field of ABPP.
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Affiliation(s)
- Lianne I Willems
- Leiden University , Leiden Institute of Chemistry, Gorlaeus Laboratories, Einsteinweg 55, 2333 CC Leiden, The Netherlands
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133
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Abstract
Monitoring the activity of a caspase, either as an isolated protein or in a complex mixture (e.g., a cytosolic extract), can be achieved by measuring substrate cleavage. Chromogenic or fluorogenic substrates are available for many caspases. These substrates usually consist of the four-amino-acid motif that is optimal for each caspase and a moiety that, when cleaved, generates either a chromophore or a fluorophore that can be detected using spectrophotometric or fluorimetric means. In this protocol, we describe how to use these substrates to monitor caspase activity in samples containing active caspases (e.g., apoptotic cells). Caspase inhibitors, which contain a moiety that covalently attaches to the active site of the caspase, can be used in these assays. These assays will ascertain whether caspases are involved in a specific process (e.g., whether caspases are activated after an apoptotic stimulus) and are particularly informative if a purified caspase is used. However, the substrates and inhibitors are not specific for a particular caspase in an environment containing multiple caspases. So, if cytosolic or apoptotic cell extracts are used in these assays, additional experiments must be performed to identify exactly which caspases are involved.
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Affiliation(s)
- Gavin P McStay
- Department of Life Sciences, New York Institute of Technology, Old Westbury, New York 11568
| | - Douglas R Green
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105
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134
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Jung HK, Wang K, Jung MK, Kim IS, Lee BH. In vivo near-infrared fluorescence imaging of apoptosis using histone H1-targeting peptide probe after anti-cancer treatment with cisplatin and cetuximab for early decision on tumor response. PLoS One 2014; 9:e100341. [PMID: 24949860 PMCID: PMC4065102 DOI: 10.1371/journal.pone.0100341] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 05/23/2014] [Indexed: 12/29/2022] Open
Abstract
Early decision on tumor response after anti-cancer treatment is still an unmet medical need. Here we investigated whether in vivo imaging of apoptosis using linear and cyclic (disulfide-bonded) form of ApoPep-1, a peptide that recognizes histone H1 exposed on apoptotic cells, at an early stage after treatment could predict tumor response to the treatment later. Treatment of stomach tumor cells with cistplatin or cetuximab alone induced apoptosis, while combination of cisplatin plus cetuximab more efficiently induced apoptosis, as detected by binding with linear and cyclic form of ApoPep-1. However, the differences between the single agent and combination treatment were more remarkable as detected with the cyclic form compared to the linear form. In tumor-bearing mice, apoptosis imaging was performed 1 week and 2 weeks after the initiation of treatment, while tumor volumes and weights were measured 3 weeks after the treatment. In vivo fluorescence imaging signals obtained by the uptake of ApoPep-1 to tumor was most remarkable in the group injected with cyclic form of ApoPep-1 at 1 week after combined treatment with cisplatin plus cetuximab. Correlation analysis revealed that imaging signals by cyclic ApoPep-1 at 1 week after treatment with cisplatin plus cetuximab in combination were most closely related with tumor volume changes (r2 = 0.934). These results demonstrate that in vivo apoptosis imaging using Apopep-1, especially cyclic ApoPep-1, is a sensitive and predictive tool for early decision on stomach tumor response after anti-cancer treatment.
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Affiliation(s)
- Hyun-Kyung Jung
- Department of Biochemistry and Cell Biology and School of Medicine, Kyungpook National University, Daegu, Korea
- BK21 Plus KNU Biomedical Convergence Program, Department of Biomedical Science, Graduate School, Kyungpook National University, Daegu, Korea
| | - Kai Wang
- Department of Plastic Surgery, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Min Kyu Jung
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Korea
| | - In-San Kim
- Department of Biochemistry and Cell Biology and School of Medicine, Kyungpook National University, Daegu, Korea
- BK21 Plus KNU Biomedical Convergence Program, Department of Biomedical Science, Graduate School, Kyungpook National University, Daegu, Korea
| | - Byung-Heon Lee
- Department of Biochemistry and Cell Biology and School of Medicine, Kyungpook National University, Daegu, Korea
- BK21 Plus KNU Biomedical Convergence Program, Department of Biomedical Science, Graduate School, Kyungpook National University, Daegu, Korea
- * E-mail:
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135
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Su H, Chen G, Gangadharmath U, Gomez LF, Liang Q, Mu F, Mocharla VP, Szardenings AK, Walsh JC, Xia CF, Yu C, Kolb HC. Evaluation of [(18)F]-CP18 as a PET imaging tracer for apoptosis. Mol Imaging Biol 2014; 15:739-47. [PMID: 23681757 DOI: 10.1007/s11307-013-0644-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
PURPOSE We identified and validated [(18)F]-CP18, a DEVD (the caspase 3 substrate recognition motif) containing substrate-based compound as an imaging tracer for caspase-3 activity in apoptotic cells. PROCEDURES CP18 was radiolabeled with fluorine-18 using click chemistry. The affinity and selectivity of CP18 for caspase-3 were evaluated in vitro. The biodistribution and metabolism pattern of [(18)F]-CP18 were assessed in vivo. [(18)F]-CP18 positron emission tomography (PET) scans were performed in a dexamethasone-induced thymic apoptosis mouse model. After imaging, the mice were sacrificed, and individual organs were collected, measured in a gamma counter, and tested for caspase-3 activity. RESULTS In vitro enzymatic caspase-3 assay demonstrated specific cleavage of CP18. In vivo, [(18)F]-CP18 is predominantly cleared through the kidneys and urine, and is rapidly eliminated from the bloodstream. There was a sixfold increase in caspase activity and a fourfold increase of [(18)F]-CP18 retention in the dexamethasone-induced thymus of treated versus control mice. CONCLUSIONS We report the use [(18)F]-CP18 as a PET tracer for imaging apoptosis. Our data support further development of this tracer for clinical PET applications.
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Affiliation(s)
- Helen Su
- Molecular Imaging Biomarker Research, Siemens Medical Solutions USA, Inc, 6100 Bristol Parkway, Culver City, CA, 90230, USA
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136
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Lim NH, Meinjohanns E, Bou-Gharios G, Gompels LL, Nuti E, Rossello A, Devel L, Dive V, Meldal M, Nagase H. In vivo imaging of matrix metalloproteinase 12 and matrix metalloproteinase 13 activities in the mouse model of collagen-induced arthritis. Arthritis Rheumatol 2014; 66:589-98. [PMID: 24574219 DOI: 10.1002/art.38295] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 11/21/2013] [Indexed: 11/05/2022]
Abstract
OBJECTIVE To develop enzyme-activatable Förster resonance energy transfer (FRET) substrate probes to detect matrix metalloproteinase 12 (MMP-12) and MMP-13 activities in vivo in mouse models of inflammatory arthritis. METHODS Peptidic FRET probes activated by MMP-12 and MMP-13 were reverse designed from inhibitors selected from a phosphinic peptide inhibitor library. Selectivity of the probes was demonstrated in vitro using MMP-1, MMP-2, MMP-3, MMP-12, and MMP-13. In vivo activation of the probes was tested in the zymosan-induced mouse model of inflammation, and probe specificity was evaluated by the MMP inhibitor GM6001 and specific synthetic inhibitors of MMP-12 and MMP-13. The probes were used to monitor these enzyme activities in the collagen-induced arthritis (CIA) model in vivo. RESULTS The MMP-12 and MMP-13 activity probes (MMP12ap and MMP13ap, respectively) discriminated between the activities of the 2 enzymes. The in vivo activation of these probes was inhibited by GM6001 and by their respective specific inhibitors. In the CIA model, MMP12ap activation peaked 5 days after disease onset and showed strong correlation with disease severity during this time (r = 0.85, P < 0.0001). MMP13ap activation increased gradually after disease onset and correlated with disease severity over a longer period of 15 days (r = 0.58, P < 0.0001). CONCLUSION We generated two selective FRET probes that can be used to monitor MMP-12 and MMP-13 activities in live animals. MMP12ap follows the initial stage of inflammation in CIA, while MMP13ap follows the progression of the disease. The specificity of these probes is useful in monitoring the efficacy of MMP inhibitors.
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Affiliation(s)
- Ngee Han Lim
- Kennedy Institute of Rheumatology and University of Oxford, Oxford, UK
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137
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Ye D, Shuhendler AJ, Cui L, Tong L, Tee SS, Tikhomirov G, Felsher DW, Rao J. Bioorthogonal cyclization-mediated in situ self-assembly of small-molecule probes for imaging caspase activity in vivo. Nat Chem 2014; 6:519-26. [PMID: 24848238 PMCID: PMC4031611 DOI: 10.1038/nchem.1920] [Citation(s) in RCA: 352] [Impact Index Per Article: 35.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 03/13/2014] [Indexed: 02/06/2023]
Abstract
Directed self-assembly of small molecules in living systems could enable a myriad of applications in biology and medicine, and it has been widely used to synthesize supramolecules and nano/microstructures in solution and in living cells. However, controlling self-assembly of synthetic small molecules in living animals is challenging because of the complex and dynamic in vivo physiological environment. Here we employed an optimized first-order bioorthogonal cyclization reaction to control self-assembly of a fluorescent small molecule, and demonstrated its in vivo applicability by imaging of casapae-3/7 activity in human tumor xenograft mouse models of chemotherapy. The in situ assembled fluorescent nanoparticles have been successfully imaged in both apoptotic cells and tumor tissues using three-dimensional structured illumination microscopy. This strategy combines the advantages offered by small molecules with those of nanomaterials and should find widespread use for non-invasive imaging of enzyme activity in vivo.
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Affiliation(s)
- Deju Ye
- 1] Molecular Imaging Program at Stanford, Departments of Radiology and Chemistry, Stanford University, Stanford, California 94305-5484, USA [2]
| | - Adam J Shuhendler
- 1] Molecular Imaging Program at Stanford, Departments of Radiology and Chemistry, Stanford University, Stanford, California 94305-5484, USA [2]
| | - Lina Cui
- Molecular Imaging Program at Stanford, Departments of Radiology and Chemistry, Stanford University, Stanford, California 94305-5484, USA
| | - Ling Tong
- Departments of Medicine and Pathology, Division of Oncology, School of Medicine Stanford University, Stanford, California, 94305-5151, USA
| | - Sui Seng Tee
- Molecular Imaging Program at Stanford, Departments of Radiology and Chemistry, Stanford University, Stanford, California 94305-5484, USA
| | - Grigory Tikhomirov
- Molecular Imaging Program at Stanford, Departments of Radiology and Chemistry, Stanford University, Stanford, California 94305-5484, USA
| | - Dean W Felsher
- Departments of Medicine and Pathology, Division of Oncology, School of Medicine Stanford University, Stanford, California, 94305-5151, USA
| | - Jianghong Rao
- Molecular Imaging Program at Stanford, Departments of Radiology and Chemistry, Stanford University, Stanford, California 94305-5484, USA
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138
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Abstract
The coordination of cell proliferation and programmed death (apoptosis) is essential for normal physiology, and imbalance in these two opposing processes is implicated in various diseases. Objective and quantitative noninvasive imaging of apoptosis would significantly facilitate rapid screening as well as validation of therapeutic chemicals. Herein, we molecularly engineered an apoptosis switch-on PET-based cyclic herpes simplex virus type 1-thymidine kinase reporter (cTK266) containing a caspase-3 recognition domain as the switch. Translation of the reporter and protein splicing in healthy mammalian cells produce an inactive cyclic chimera. Upon apoptosis, caspase-3-specific cleavage of the circular product occurs, resulting in the restoration of the thymidine kinase activity, which can be detected in living cells and animals by noninvasive PET imaging. Our results showed the high sensitivity of this reporter in dynamic and quantitative imaging of apoptosis in living subjects. This reporter could be applied as a valuable tool for high-throughput functional screening of proapoptotic and antiapoptotic compounds in preclinical models in drug development, and monitoring the destination of therapeutic cells in clinical settings.
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139
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Hunerdosse D, Nomura DK. Activity-based proteomic and metabolomic approaches for understanding metabolism. Curr Opin Biotechnol 2014; 28:116-26. [PMID: 24594637 DOI: 10.1016/j.copbio.2014.02.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 01/30/2014] [Accepted: 02/03/2014] [Indexed: 12/20/2022]
Abstract
There are an increasing number of human pathologies that have been associated with altered metabolism, including obesity, diabetes, atherosclerosis, cancer, and neurodegenerative diseases. Most attention on metabolism has been focused on well-understood metabolic pathways and has largely ignored most of the biochemical pathways that operate in (patho)physiological settings, in part because of the vast landscape of uncharacterized and undiscovered metabolic pathways. One technology that has arisen to meet this challenge is activity-based protein profiling (ABPP) that uses activity-based chemical probes to broadly assess the functional states of both characterized and uncharacterized enzymes. This review will focus on how ABPP, coupled with inhibitor discovery platforms and functional metabolomic technologies, have led to discoveries that have expanded our knowledge of metabolism in health and disease.
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Affiliation(s)
- Devon Hunerdosse
- Program in Metabolic Biology, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Daniel K Nomura
- Program in Metabolic Biology, University of California, Berkeley, Berkeley, CA 94720, United States.
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140
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Chen ZY, Wang YX, Lin Y, Zhang JS, Yang F, Zhou QL, Liao YY. Advance of molecular imaging technology and targeted imaging agent in imaging and therapy. BIOMED RESEARCH INTERNATIONAL 2014; 2014:819324. [PMID: 24689058 PMCID: PMC3943245 DOI: 10.1155/2014/819324] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2013] [Revised: 12/29/2013] [Accepted: 12/30/2013] [Indexed: 02/06/2023]
Abstract
Molecular imaging is an emerging field that integrates advanced imaging technology with cellular and molecular biology. It can realize noninvasive and real time visualization, measurement of physiological or pathological process in the living organism at the cellular and molecular level, providing an effective method of information acquiring for diagnosis, therapy, and drug development and evaluating treatment of efficacy. Molecular imaging requires high resolution and high sensitive instruments and specific imaging agents that link the imaging signal with molecular event. Recently, the application of new emerging chemical technology and nanotechnology has stimulated the development of imaging agents. Nanoparticles modified with small molecule, peptide, antibody, and aptamer have been extensively applied for preclinical studies. Therapeutic drug or gene is incorporated into nanoparticles to construct multifunctional imaging agents which allow for theranostic applications. In this review, we will discuss the characteristics of molecular imaging, the novel imaging agent including targeted imaging agent and multifunctional imaging agent, as well as cite some examples of their application in molecular imaging and therapy.
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Affiliation(s)
- Zhi-Yi Chen
- Department of Ultrasound Medicine, Laboratory of Ultrasound Molecular Imaging, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510150, China
| | - Yi-Xiang Wang
- Department of Imaging and Interventional Radiology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Yan Lin
- Department of Ultrasound Medicine, Laboratory of Ultrasound Molecular Imaging, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510150, China
| | - Jin-Shan Zhang
- Department of Nuclear Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510150, China
| | - Feng Yang
- Department of Ultrasound Medicine, Laboratory of Ultrasound Molecular Imaging, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510150, China
| | - Qiu-Lan Zhou
- Department of Ultrasound Medicine, Laboratory of Ultrasound Molecular Imaging, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510150, China
| | - Yang-Ying Liao
- Department of Ultrasound Medicine, Laboratory of Ultrasound Molecular Imaging, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510150, China
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141
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van Domselaar R, de Poot SAH, Bovenschen N. Proteomic profiling of proteases: tools for granzyme degradomics. Expert Rev Proteomics 2014; 7:347-59. [DOI: 10.1586/epr.10.24] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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142
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Abstract
Caspases are a family of integral proteases playing a role in apoptosis. The importance of apoptosis in disease has made these proteases not only an attractive drug target but also a focal point for measuring apoptosis in vivo. The critical role caspases play in determining cell death has led to the development of a wide array of technologies to measure caspase activity in vivo, ranging from small molecule PET imaging reagents to fluorescent and luminescent protein-based reporters used in whole animal and cell-based applications. This chapter reviews this wide range of technologies available as well as the most appropriate applications for each reagent and the mechanism of how it measures caspase activity in vivo.
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Affiliation(s)
- Samantha B Nicholls
- MassGeneral Institute for Neurodegenerative Disease, Department of Neurology, Alzheimer's Disease Research Laboratory, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts, USA
| | - Bradley T Hyman
- MassGeneral Institute for Neurodegenerative Disease, Department of Neurology, Alzheimer's Disease Research Laboratory, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts, USA.
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143
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Wang MW, Wang F, Zheng YJ, Zhang YJ, Zhang YP, Zhao Q, Shen CKF, Wang Y, Sun SH. An in vivo molecular imaging probe (18)F-Annexin B1 for apoptosis detection by PET/CT: preparation and preliminary evaluation. Apoptosis 2013; 18:238-47. [PMID: 23238992 DOI: 10.1007/s10495-012-0788-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
There is an increasing need to develop non-invasive molecular imaging strategies for visualizing and quantifying apoptosis status of diseases (especially for cancer) for diagnosis and monitoring treatment response. Since externalization of phosphatidylserine (PS) is one of the early molecular events during apoptosis, Annexin B1 (AnxB1), a member of Annexins family with high affinity toward the head group of PS, could be a potential positron emission tomography (PET) imaging probe for imaging cell death process after labeled by positron-emitting nuclides, such as (18)F. In the present study, we investigated a novel PET probe, (18)F-labeled Annexin B1 ((18)F-AnxB1), for apoptosis imaging. (18)F-AnxB1 was prepared reliably by conjugating AnxB1 with a (18)F-tag, N-succinimidyl 4-[(18)F]fluorobenzoate ([(18)F]SFB), in a radiolabeling yield of about 20 % within 40 min. The in vitro binding of (18)F-AnxB1 with apoptotic cells induced by anti-Fas antibody showed twofold increase compared to those without treatment, confirmed by flow cytometric analysis with AnxV-FITC/PI staining. Stability tests demonstrated (18)F-AnxB1 was rather stable in vitro and in vivo without degradation. The serial (18)F-AnxB1 PET/CT scans in healthy rats outlined its biodistribution and pharmacokinetics, indicating a rapid renal clearance and predominant accumulation into kidney and bladder at 2 h p.i. (18)F-AnxB1 PET/CT imaging was successfully applied to visualize in vivo apoptosis sites in tumor induced by chemotherapy and in kidney simulated by ischemia-reperfusion injury. The high-contrast images were obtained at 2 h p.i. to delineate apoptotic tumor. Apoptotic region could be still identified by (18)F-AnxB1 PET 4 h p.i., despite the high probe retention in kidneys. In summary, we have developed (18)F-AnxB1 as a PS-specific PET probe for the apoptosis detection and quantification which could have broad applications from disease diagnosis to treatment monitoring, especially in the cases of cancer.
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Affiliation(s)
- Ming-Wei Wang
- PET Center, Department of Nuclear Medicine, Fudan University Shanghai Cancer Center, Shanghai 200032, China
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144
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Shen B, Jeon J, Palner M, Ye D, Shuhendler A, Chin FT, Rao J. Positron emission tomography imaging of drug-induced tumor apoptosis with a caspase-triggered nanoaggregation probe. Angew Chem Int Ed Engl 2013; 52:10511-4. [PMID: 23881906 PMCID: PMC4077287 DOI: 10.1002/anie.201303422] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Indexed: 11/07/2022]
Abstract
Drug Design: An (18)F-labeled caspase-3-sensitive nanoaggregation positron emission tomography tracer was prepared and evaluated for imaging the caspase-3 activity in doxorubicin-treated tumor xenografts. Enhanced retention of the (18)F activity in apoptotic tumors is achieved through intramolecular macrocyclization and in situ aggregation upon caspase-3 activation (see picture).
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Affiliation(s)
| | | | - Mikael Palner
- Department of Radiology, Molecular Imaging Program at Stanford, Stanford University School of Medicine, Stanford, CA 94305-5484, USA
| | - Deju Ye
- Department of Radiology, Molecular Imaging Program at Stanford, Stanford University School of Medicine, Stanford, CA 94305-5484, USA
| | - Adam Shuhendler
- Department of Radiology, Molecular Imaging Program at Stanford, Stanford University School of Medicine, Stanford, CA 94305-5484, USA
| | - Frederick T. Chin
- Department of Radiology, Molecular Imaging Program at Stanford, Stanford University School of Medicine, Stanford, CA 94305-5484, USA
| | - Jianghong Rao
- Department of Radiology, Molecular Imaging Program at Stanford, Stanford University School of Medicine, Stanford, CA 94305-5484, USA
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145
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Puri AW, Bogyo M. Applications of small molecule probes in dissecting mechanisms of bacterial virulence and host responses. Biochemistry 2013; 52:5985-96. [PMID: 23937332 DOI: 10.1021/bi400854d] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Elucidating the molecular and biochemical details of bacterial infections can be challenging because of the many complex interactions that exist between a pathogen and its host. Consequently, many tools have been developed to aid the study of bacterial pathogenesis. Small molecules are a valuable complement to traditional genetic techniques because they can be used to rapidly perturb genetically intractable systems and to monitor post-translationally regulated processes. Activity-based probes are a subset of small molecules that covalently label an enzyme of interest based on its catalytic mechanism. These tools allow monitoring of enzyme activation within the context of a native biological system and can be used to dissect the biochemical details of enzyme function. This review describes the development and application of activity-based probes for examining aspects of bacterial infection on both sides of the host-pathogen interface.
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Affiliation(s)
- Aaron W Puri
- Department of Chemical and Systems Biology, ‡Department of Microbiology and Immunology, and §Department of Pathology, Stanford University School of Medicine , 300 Pasteur Drive, Stanford, California 94305, United States
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146
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Poreba M, Strózyk A, Salvesen GS, Drag M. Caspase substrates and inhibitors. Cold Spring Harb Perspect Biol 2013; 5:a008680. [PMID: 23788633 DOI: 10.1101/cshperspect.a008680] [Citation(s) in RCA: 133] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Caspases are proteases at the heart of networks that govern apoptosis and inflammation. The past decade has seen huge leaps in understanding the biology and chemistry of the caspases, largely through the development of synthetic substrates and inhibitors. Such agents are used to define the role of caspases in transmitting life and death signals, in imaging caspases in situ and in vivo, and in deconvoluting the networks that govern cell behavior. Additionally, focused proteomics methods have begun to reveal the natural substrates of caspases in the thousands. Together, these chemical and proteomics technologies are setting the scene for designing and implementing control of caspase activity as appropriate targets for disease therapy.
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Affiliation(s)
- Marcin Poreba
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Technology, 50-370 Wrocław, Poland
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147
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Xie J, Wang C, Virostko J, Manning HC, Pham W, Bauer J, Gore JC. A novel reporter system for molecular imaging and high-throughput screening of anticancer drugs. Chembiochem 2013; 14:1494-503. [PMID: 23881799 DOI: 10.1002/cbic.201300142] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Indexed: 11/11/2022]
Abstract
Apoptosis is irreversible programmed cell death, characterized by a cellular cascade activation of caspase 3, which subsequently degrades proteins and other components of cells with a motif sequence. Here we report a novel reporter system to detect apoptosis, growth arrest, and cell death based on controlled and self-amplified protein degradation. The key element of the reporter system is an apoptotic sensor chimerical protein which consists of three components: procaspase 3, ubiquitin (Ub), and a strong consensus sequence of N-degron. Between each of these units is a DEVD (Asp-Glu-Val-Asp) sequence, which acts as the cleavage target of caspase 3. This non-conventional signal loss approach is much more sensitive than other native methods that are based on signal gain. The superior sensitivity is demonstrated by its effective application in 386-well high-throughput screening (HTS) with low drug concentrations and a short incubation time. The HTS selection process using this reporter system is very simple and economic. The simplicity eliminates potential errors introduced by multiple steps; there is no need for any substrate. Furthermore, the cells in the assay need not be disrupted, and the morphology of the cells can provide additional information on mechanisms. After HTS, the intact cells can also be used for other analytic analysis. This system thus has a potentially important role in the discovery and development of new anticancer drugs. It also appears to be very versatile, can be used both in vitro and in vivo with different linked reporter genes, and can be used for a variety of imaging applications.
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Affiliation(s)
- Jingping Xie
- Institute of Imaging Science, Vanderbilt University, Nashville, TN 37232, USA.
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148
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Shen B, Jeon J, Palner M, Ye D, Shuhendler A, Chin FT, Rao J. Positron Emission Tomography Imaging of Drug-Induced Tumor Apoptosis with a Caspase-Triggered Nanoaggregation Probe. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201303422] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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149
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Vickers CJ, González-Páez GE, Wolan DW. Selective detection of caspase-3 versus caspase-7 using activity-based probes with key unnatural amino acids. ACS Chem Biol 2013; 8:1558-66. [PMID: 23614665 DOI: 10.1021/cb400209w] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Caspases are required for essential biological functions, most notably apoptosis and pyroptosis, but also cytokine production, cell proliferation, and differentiation. One of the most well studied members of this cysteine protease family includes executioner caspase-3, which plays a central role in cell apoptosis and differentiation. Unfortunately, there exists a dearth of chemical tools to selectively monitor caspase-3 activity under complex cellular and in vivo conditions due to its close homology with executioner caspase-7. Commercially available activity-based probes and substrates rely on the canonical DEVD tetrapeptide sequence, which both caspases-3 and -7 recognize with similar affinity, and thus the individual contributions of caspase-3 and/or -7 toward important cellular processes are irresolvable. Here, we analyzed a variety of permutations of the DEVD peptide sequence in order to discover peptides with biased activity and recognition of caspase-3 versus caspases-6, -7, -8, and -9. Through this study, we identify fluorescent and biotinylated probes capable of selective detection of caspase-3 using key unnatural amino acids. Likewise, we determined the X-ray crystal structures of caspases-3, -7, and -8 in complex with our lead peptide inhibitor to elucidate the binding mechanism and active site interactions that promote the selective recognition of caspase-3 over other highly homologous caspase family members.
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Affiliation(s)
- Chris J. Vickers
- Departments of Molecular
and Experimental Medicine
and Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Gonzalo E. González-Páez
- Departments of Molecular
and Experimental Medicine
and Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Dennis W. Wolan
- Departments of Molecular
and Experimental Medicine
and Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, United States
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150
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Vickers CJ, González-Páez GE, Umotoy JC, Cayanan-Garrett C, Brown SJ, Wolan DW. Small-molecule procaspase activators identified using fluorescence polarization. Chembiochem 2013; 14:1419-22. [PMID: 23836614 DOI: 10.1002/cbic.201300315] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Indexed: 01/17/2023]
Abstract
Wake up, protein! Small molecules that directly activate proteins are rare and their discovery opens new avenues for the development of drugs and chemical tools to probe the functions and mechanisms of protein targets. To address the one-sided dichotomy between enzyme inhibition and activation, we describe a series of procaspase activators as chemical tools in the study of caspase biology.
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Affiliation(s)
- Chris J Vickers
- Department of Molecular and Experimental Medicine and Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, USA
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