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Zhao W, Cui H, Liu K, Yang X, Xing S, Li W. Unveiling Anti-Diabetic Potential of Baicalin and Baicalein from Baikal Skullcap: LC-MS, In Silico, and In Vitro Studies. Int J Mol Sci 2024; 25:3654. [PMID: 38612466 PMCID: PMC11011639 DOI: 10.3390/ijms25073654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 03/19/2024] [Accepted: 03/22/2024] [Indexed: 04/14/2024] Open
Abstract
Type 2 diabetes mellitus (T2DM) is marked by persistent hyperglycemia, insulin resistance, and pancreatic β-cell dysfunction, imposing substantial health burdens and elevating the risk of systemic complications and cardiovascular diseases. While the pathogenesis of diabetes remains elusive, a cyclical relationship between insulin resistance and inflammation is acknowledged, wherein inflammation exacerbates insulin resistance, perpetuating a deleterious cycle. Consequently, anti-inflammatory interventions offer a therapeutic avenue for T2DM management. In this study, a herb called Baikal skullcap, renowned for its repertoire of bioactive compounds with anti-inflammatory potential, is posited as a promising source for novel T2DM therapeutic strategies. Our study probed the anti-diabetic properties of compounds from Baikal skullcap via network pharmacology, molecular docking, and cellular assays, concentrating on their dual modulatory effects on diabetes through Protein Tyrosine Phosphatase 1B (PTP1B) enzyme inhibition and anti-inflammatory actions. We identified the major compounds in Baikal skullcap using liquid chromatography-mass spectrometry (LC-MS), highlighting six flavonoids, including the well-studied baicalein, as potent inhibitors of PTP1B. Furthermore, cellular experiments revealed that baicalin and baicalein exhibited enhanced anti-inflammatory responses compared to the active constituents of licorice, a known anti-inflammatory agent in TCM. Our findings confirmed that baicalin and baicalein mitigate diabetes via two distinct pathways: PTP1B inhibition and anti-inflammatory effects. Additionally, we have identified six flavonoid molecules with substantial potential for drug development, thereby augmenting the T2DM pharmacotherapeutic arsenal and promoting the integration of herb-derived treatments into modern pharmacology.
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Affiliation(s)
| | | | | | | | - Shu Xing
- Edmond H. Fischer Signal Transduction Laboratory, Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China; (W.Z.); (H.C.); (K.L.); (X.Y.)
| | - Wannan Li
- Edmond H. Fischer Signal Transduction Laboratory, Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China; (W.Z.); (H.C.); (K.L.); (X.Y.)
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2
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Li A, Bouhss A, Clément MJ, Bauvais C, Taylor JP, Bollot G, Pastré D. Using the structural diversity of RNA: protein interfaces to selectively target RNA with small molecules in cells: methods and perspectives. Front Mol Biosci 2023; 10:1298441. [PMID: 38033386 PMCID: PMC10687564 DOI: 10.3389/fmolb.2023.1298441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 10/24/2023] [Indexed: 12/02/2023] Open
Abstract
In recent years, RNA has gained traction both as a therapeutic molecule and as a therapeutic target in several human pathologies. In this review, we consider the approach of targeting RNA using small molecules for both research and therapeutic purposes. Given the primary challenge presented by the low structural diversity of RNA, we discuss the potential for targeting RNA: protein interactions to enhance the structural and sequence specificity of drug candidates. We review available tools and inherent challenges in this approach, ranging from adapted bioinformatics tools to in vitro and cellular high-throughput screening and functional analysis. We further consider two critical steps in targeting RNA/protein interactions: first, the integration of in silico and structural analyses to improve the efficacy of molecules by identifying scaffolds with high affinity, and second, increasing the likelihood of identifying on-target compounds in cells through a combination of high-throughput approaches and functional assays. We anticipate that the development of a new class of molecules targeting RNA: protein interactions to prevent physio-pathological mechanisms could significantly expand the arsenal of effective therapeutic compounds.
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Affiliation(s)
- Aixiao Li
- Synsight, Genopole Entreprises, Evry, France
| | - Ahmed Bouhss
- Université Paris-Saclay, INSERM U1204, Université d’Évry, Structure-Activité des Biomolécules Normales et Pathologiques (SABNP), Evry, France
| | - Marie-Jeanne Clément
- Université Paris-Saclay, INSERM U1204, Université d’Évry, Structure-Activité des Biomolécules Normales et Pathologiques (SABNP), Evry, France
| | | | - J. Paul Taylor
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | | | - David Pastré
- Université Paris-Saclay, INSERM U1204, Université d’Évry, Structure-Activité des Biomolécules Normales et Pathologiques (SABNP), Evry, France
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3
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Delompré T, Belloir C, Martin C, Salles C, Briand L. Detection of Bitterness in Vitamins Is Mediated by the Activation of Bitter Taste Receptors. Nutrients 2022; 14:nu14194141. [PMID: 36235793 PMCID: PMC9571608 DOI: 10.3390/nu14194141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 09/23/2022] [Accepted: 09/29/2022] [Indexed: 11/05/2022] Open
Abstract
Vitamins are known to generate bitterness, which may contribute to an off-taste or aftertaste for some nutritional supplements. This negative sensation can lead to a reduction in their consumption. Little is known about the bitter taste threshold and taste sensing system for the bitter taste detection of vitamins. To better understand the mechanisms involved in bitterness perception, we combined taste receptor functional assays and sensory analysis. In humans, bitter taste detection is mediated by 25 G-protein-coupled receptors belonging to the TAS2R family. First, we studied the bitterness of thirteen vitamins using a cellular-based functional taste receptor assay. We found four vitamins that can stimulate one or more TAS2Rs. For each positive molecule-receptor combination, we tested seven increasing concentrations to determine the half-maximal effective concentration (EC50) and the cellular bitter taste threshold. Second, we measured the bitter taste detection threshold for four vitamins that exhibit a strong bitter taste using a combination of ascending series and sensory difference tests. A combination of sensory and biological data can provide useful results that explain the perception of vitamin bitterness and its real contribution to the off-taste of nutritional supplements.
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Jaron M, Lehky M, Zarà M, Zaydowicz CN, Lak A, Ballmann R, Heine PA, Wenzel EV, Schneider KT, Bertoglio F, Kempter S, Köster RW, Barbieri SS, van den Heuvel J, Hust M, Dübel S, Schubert M. Baculovirus-Free SARS-CoV-2 Virus-like Particle Production in Insect Cells for Rapid Neutralization Assessment. Viruses 2022. [PMID: 36298643 DOI: 10.3390/v14102087/s1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023] Open
Abstract
Virus-like particles (VLPs) resemble authentic virus while not containing any genomic information. Here, we present a fast and powerful method for the production of SARS-CoV-2 VLP in insect cells and the application of these VLPs to evaluate the inhibition capacity of monoclonal antibodies and sera of vaccinated donors. Our method avoids the baculovirus-based approaches commonly used in insect cells by employing direct plasmid transfection to co-express SARS-CoV-2 envelope, membrane, and spike protein that self-assemble into VLPs. After optimization of the expression plasmids and vector ratios, VLPs with an ~145 nm diameter and the typical "Corona" aura were obtained, as confirmed by nanoparticle tracking analysis (NTA) and transmission electron microscopy (TEM). Fusion of the membrane protein to GFP allowed direct quantification of binding inhibition to angiotensin II-converting enzyme 2 (ACE2) on cells by therapeutic antibody candidates or sera from vaccinated individuals. Neither VLP purification nor fluorescent labeling by secondary antibodies are required to perform these flow cytometric assays.
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Affiliation(s)
- Marcel Jaron
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Michael Lehky
- Recombinant Protein Expression Platform, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Marta Zarà
- Unit of Brain-Heart Axis, IRCCS Monzino Cardiology Center, Via C. Parea 4, 20138 Milano, Italy
| | - Chris Nicole Zaydowicz
- Division of Cellular and Molecular Neurobiology, Zoological Institute, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Aidin Lak
- Institute for Electrical Measurement Science and Fundamental Electrical Engineering, Technische Universität Braunschweig, Hans-Sommer-Straße 66, 38106 Braunschweig, Germany
| | - Rico Ballmann
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Philip Alexander Heine
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | | | - Kai-Thomas Schneider
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Federico Bertoglio
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Susanne Kempter
- Department of Physics, Ludwig-Maximilians-Universität, Geschwister-Scholl-Platz 1, 80539 München, Germany
| | - Reinhard Wolfgang Köster
- Division of Cellular and Molecular Neurobiology, Zoological Institute, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Silvia Stella Barbieri
- Unit of Brain-Heart Axis, IRCCS Monzino Cardiology Center, Via C. Parea 4, 20138 Milano, Italy
| | - Joop van den Heuvel
- Recombinant Protein Expression Platform, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Michael Hust
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Stefan Dübel
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Maren Schubert
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
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Oeyen M, Meyen E, Doijen J, Schols D. In-Depth Characterization of Zika Virus Inhibitors Using Cell-Based Electrical Impedance. Microbiol Spectr 2022; 10:e0049122. [PMID: 35862960 PMCID: PMC9431523 DOI: 10.1128/spectrum.00491-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 06/20/2022] [Indexed: 11/30/2022] Open
Abstract
In this study, we use electric cell-substrate impedance sensing (ECIS), an established cell-based electrical impedance (CEI) technology, to decipher the kinetic cytopathic effect (CPE) induced by Zika virus (ZIKV) in susceptible human A549 lung epithelial cells and to evaluate several classes of compounds with reported antiviral activity (two entry inhibitors and two replication inhibitors). To validate the assay, we compare the results with those obtained with more traditional in vitro methods based on cell viability and viral yield readouts. We demonstrate that CEI can detect viral infection in a sensitive manner and can be used to determine antiviral potency. Moreover, CEI has multiple benefits compared to conventional assays: the technique is less laborious and better at visualizing the dynamic antiviral activity profile of the compounds, while also it has the ability to determine interesting time points that can be selected as endpoints in assays without continuous readout. We describe several parameters to characterize the compounds' cytotoxicity and their antiviral activity profile. In addition, the CEI patterns provide valuable additional information about the presumed mechanism of action of these compounds. Finally, as a proof of concept, we used CEI to evaluate the antiviral activity of a small series of compounds, for which we demonstrate that the sulfonated polymer PRO2000 inhibits ZIKV with a response profile representative for a viral entry inhibitor. Overall, we demonstrate for the first time that CEI is a powerful technology to evaluate and characterize compounds against ZIKV replication in a real-time, label-free, and noninvasive manner. IMPORTANCE Zika virus can cause serious disease in humans. Unfortunately, no antiviral drugs are available to treat infection. Here, we use an impedance-based method to continuously monitor virus infection in-and damage to-human cells. We can determine the Zika viral dose with this technique and also evaluate whether antiviral compounds protect the cells from damage caused by virus replication. We also show that this technique can be used to further unravel the characteristics of these compounds, such as their toxicity to the cells, and that it might even give further insight in their mechanism of antiviral action. Finally, we also find a novel Zika virus inhibitor, PRO2000. Overall, in this study, we use the impedance technology to-for the first time-evaluate compounds with anti-Zika virus properties, and therefore it can add valuable information in the further search for antiviral drugs.
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Affiliation(s)
- Merel Oeyen
- Katholieke Universiteit Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Eef Meyen
- Katholieke Universiteit Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Jordi Doijen
- Katholieke Universiteit Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Dominique Schols
- Katholieke Universiteit Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven, Belgium
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6
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Abstract
Increasing interest in studying and modulating the interactions between RNAs and their RNA-binding proteins has indicated the need for enabling technologies. Existing means of detecting RNA-protein interactions (RPIs) are often limited to biochemical or post-lysis methods or cell-based methods that require the addition of an RNA-based affinity tag, such as the MS2 hairpin, precluding them from use in detecting small or highly processed RNAs. Taking advantage of bioorthogonal chemistry- and split-luciferase-based technologies, we developed an assay for the detection of RPIs in live cells. This article details the protocol and design considerations for RiPCA, or RNA interaction with Protein-mediated Complementation Assay. © 2022 Wiley Periodicals LLC.
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Affiliation(s)
| | - Amanda L. Garner
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI,Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI
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7
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Głów D, Meyer S, García Roldán I, Akingunsade LM, Riecken K, Fehse B. LATE-a novel sensitive cell-based assay for the study of CRISPR/Cas9-related long-term adverse treatment effects. Mol Ther Methods Clin Dev 2021; 22:249-262. [PMID: 34485609 PMCID: PMC8399046 DOI: 10.1016/j.omtm.2021.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 07/23/2021] [Indexed: 11/26/2022]
Abstract
Since the introduction of clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9), genome editing has been broadly applied in basic research and applied biotechnology, whereas translation into clinical testing has raised safety concerns. Indeed, although frequencies and locations of off-target events have been widely addressed, little is known about their potential biological consequences in large-scale long-term settings. We have developed a long-term adverse treatment effect (LATE) in vitro assay that addresses potential toxicity of designer nucleases by assessing cell transformation events. In small-scale proof-of-principle experiments we reproducibly detected low-frequency (<0.5%) growth-promoting events in primary human newborn foreskin fibroblasts (NUFF cells) resulting from off-target cleavage in the TP53 gene. Importantly, the LATE assay detected not only off-target effects in TP53 not predicted by popular online tools but also growth-promoting mutations in other tumor suppressor genes, such as p21 and PLZF. It convincingly verified strongly reduced off-target activities of high fidelity compared with first-generation Cas9. Finally, the LATE assay was readily adapted to other cell types, namely clinically relevant human mesenchymal stromal cells (hMSCs) and retinal pigmented epithelial (RPE-1) cells. In conclusion, the LATE assay allows assessment of physiological adverse effects of the CRISPR/Cas system and might therefore be useful for preclinical safety studies.
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Affiliation(s)
- Dawid Głów
- Research Department Cell and Gene Therapy, Department of Stem Cell Transplantation, University Medical Centre Hamburg-Eppendorf (UKE), Martinistr. 52, Hamburg 20246, Germany
| | - Simon Meyer
- Research Department Cell and Gene Therapy, Department of Stem Cell Transplantation, University Medical Centre Hamburg-Eppendorf (UKE), Martinistr. 52, Hamburg 20246, Germany
| | - Irene García Roldán
- Research Department Cell and Gene Therapy, Department of Stem Cell Transplantation, University Medical Centre Hamburg-Eppendorf (UKE), Martinistr. 52, Hamburg 20246, Germany
| | - Lara Marie Akingunsade
- Research Department Cell and Gene Therapy, Department of Stem Cell Transplantation, University Medical Centre Hamburg-Eppendorf (UKE), Martinistr. 52, Hamburg 20246, Germany
| | - Kristoffer Riecken
- Research Department Cell and Gene Therapy, Department of Stem Cell Transplantation, University Medical Centre Hamburg-Eppendorf (UKE), Martinistr. 52, Hamburg 20246, Germany
| | - Boris Fehse
- Research Department Cell and Gene Therapy, Department of Stem Cell Transplantation, University Medical Centre Hamburg-Eppendorf (UKE), Martinistr. 52, Hamburg 20246, Germany
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8
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Jost C, Darowski D, Challier J, Pulko V, Hanisch LJ, Xu W, Mössner E, Bujotzek A, Klostermann S, Umana P, Kontermann RE, Klein C. CAR-J cells for antibody discovery and lead optimization of TCR-like immunoglobulins. MAbs 2020; 12:1840709. [PMID: 33136521 PMCID: PMC7646475 DOI: 10.1080/19420862.2020.1840709] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
T-cell bispecific antibodies (TCBs) are a novel class of engineered immunoglobulins that unite monovalent binding to the T-cell receptor (TCR) CD3e chain and bivalent binding to tumor-associated antigens in order to recruit and activate T-cells for tumor cell killing. In vivo, T-cell activation is usually initiated via the interaction of the TCR with the peptide-HLA complex formed by the human leukocyte antigen (HLA) and peptides derived from intracellular proteins. TCR-like antibodies (TCRLs) that recognize pHLA-epitopes extend the target space of TCBs to peptides derived from intracellular proteins, such as those overexpressed during oncogenesis or created via mutations found in cancer. One challenge during lead identification of TCRL-TCBs is to identify TCRLs that specifically, and ideally exclusively, recognize the desired pHLA, but not unrelated pHLAs. In order to identify TCRLs suitable for TCRL-TCBs, large numbers of TCRLs have to be tested in the TCB format. Here, we propose a novel approach using chimeric antigen receptors (CARs) to facilitate the identification of highly selective TCRLs. In this new so-called TCRL-CAR-J approach, TCRL-candidates are transduced as CARs into Jurkat reporter-cells, and subsequently assessed for their specificity profile. This work demonstrates that the CAR-J reporter-cell assay can be applied to predict the profile of TCRL-TCBs without the need to produce each candidate in the final TCB format. It is therefore useful in streamlining the identification of TCRL-TCBs.
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Affiliation(s)
- Christian Jost
- Roche Innovation Center Zurich, Roche Pharma Research & Early Development , Schlieren, Switzerland.,Athebio AG , Zurich, Switzerland
| | - Diana Darowski
- Roche Innovation Center Zurich, Roche Pharma Research & Early Development , Schlieren, Switzerland
| | - John Challier
- Roche Innovation Center Zurich, Roche Pharma Research & Early Development , Schlieren, Switzerland
| | - Vesna Pulko
- Roche Innovation Center Zurich, Roche Pharma Research & Early Development , Schlieren, Switzerland
| | - Lydia J Hanisch
- Roche Innovation Center Zurich, Roche Pharma Research & Early Development , Schlieren, Switzerland
| | - Wei Xu
- Roche Innovation Center Zurich, Roche Pharma Research & Early Development , Schlieren, Switzerland
| | - Ekkehard Mössner
- Roche Innovation Center Zurich, Roche Pharma Research & Early Development , Schlieren, Switzerland
| | - Alexander Bujotzek
- Roche Innovation Center Munich, Roche Pharma Research & Early Development , Penzberg, Germany
| | - Stefan Klostermann
- Roche Innovation Center Munich, Roche Pharma Research & Early Development , Penzberg, Germany
| | - Pablo Umana
- Roche Innovation Center Zurich, Roche Pharma Research & Early Development , Schlieren, Switzerland
| | | | - Christian Klein
- Roche Innovation Center Zurich, Roche Pharma Research & Early Development , Schlieren, Switzerland
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9
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Sendino M, Omaetxebarria MJ, Prieto G, Rodriguez JA. Using a Simple Cellular Assay to Map NES Motifs in Cancer-Related Proteins, Gain Insight into CRM1-Mediated NES Export, and Search for NES-Harboring Micropeptides. Int J Mol Sci 2020; 21:E6341. [PMID: 32882917 PMCID: PMC7503480 DOI: 10.3390/ijms21176341] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 08/24/2020] [Accepted: 08/26/2020] [Indexed: 12/26/2022] Open
Abstract
The nuclear export receptor CRM1 (XPO1) recognizes and binds specific sequence motifs termed nuclear export signals (NESs) in cargo proteins. About 200 NES motifs have been identified, but over a thousand human proteins are potential CRM1 cargos, and most of their NESs remain to be identified. On the other hand, the interaction of NES peptides with the "NES-binding groove" of CRM1 was studied in detail using structural and biochemical analyses, but a better understanding of CRM1 function requires further investigation of how the results from these in vitro studies translate into actual NES export in a cellular context. Here we show that a simple cellular assay, based on a recently described reporter (SRVB/A), can be applied to identify novel potential NESs motifs, and to obtain relevant information on different aspects of CRM1-mediated NES export. Using cellular assays, we first map 19 new sequence motifs with nuclear export activity in 14 cancer-related proteins that are potential CRM1 cargos. Next, we investigate the effect of mutations in individual NES-binding groove residues, providing further insight into CRM1-mediated NES export. Finally, we extend the search for CRM1-dependent NESs to a recently uncovered, but potentially vast, set of small proteins called micropeptides. By doing so, we report the first NES-harboring human micropeptides.
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Affiliation(s)
- Maria Sendino
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain;
| | - Miren Josu Omaetxebarria
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain;
| | - Gorka Prieto
- Department of Communications Engineering, University of the Basque Country (UPV/EHU), 48013 Bilbao, Spain;
| | - Jose Antonio Rodriguez
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain;
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10
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Terry-Kantor E, Tripathi A, Imberdis T, LaVoie ZM, Ho GPH, Selkoe D, Fanning S, Ramalingam N, Dettmer U. Rapid Alpha-Synuclein Toxicity in a Neural Cell Model and Its Rescue by a Stearoyl-CoA Desaturase Inhibitor. Int J Mol Sci 2020; 21:E5193. [PMID: 32707907 PMCID: PMC7432784 DOI: 10.3390/ijms21155193] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/16/2020] [Accepted: 07/16/2020] [Indexed: 01/28/2023] Open
Abstract
Genetic and biochemical evidence attributes neuronal loss in Parkinson's disease (PD) and related brain diseases to dyshomeostasis of the 14 kDa protein α-synuclein (αS). There is no consensus on how αS exerts toxicity. Explanations range from disturbed vesicle biology to proteotoxicity caused by fibrillar aggregates. To probe these mechanisms further, robust cellular toxicity models are needed, but their availability is limited. We previously reported that a shift from dynamic multimers to monomers is an early event in αS dyshomeostasis, as caused by familial PD (fPD)-linked mutants such as E46K. Excess monomers accumulate in round, lipid-rich inclusions. Engineered αS '3K' (E35K+E46K+E61K) amplifies E46K, causing a PD-like, L-DOPA-responsive motor phenotype in transgenic mice. Here, we present a cellular model of αS neurotoxicity after transducing human neuroblastoma cells to express yellow fluorescent protein (YFP)-tagged αS 3K in a doxycycline-dependent manner. αS-3K::YFP induction causes pronounced growth defects that accord with cell death. We tested candidate compounds for their ability to restore growth, and stearoyl-CoA desaturase (SCD) inhibitors emerged as a molecule class with growth-restoring capacity, but the therapeutic window varied among compounds. The SCD inhibitor MF-438 fully restored growth while exerting no apparent cytotoxicity. Our αS bioassay will be useful for elucidating compound mechanisms, for pharmacokinetic studies, and for compound/genetic screens.
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Affiliation(s)
| | | | | | | | | | | | | | - Nagendran Ramalingam
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA; (E.T.-K.); (A.T.); (T.I.); (Z.M.L.); (G.P.H.H.); (D.S.); (S.F.)
| | - Ulf Dettmer
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA; (E.T.-K.); (A.T.); (T.I.); (Z.M.L.); (G.P.H.H.); (D.S.); (S.F.)
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11
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Akinjiyan FA, Fazal A, Hild M, Beckwith REJ, Ross NT, Paulk J, Carbonneau S. A Novel Luminescence-Based High-Throughput Approach for Cellular Resolution of Protein Ubiquitination Using Tandem Ubiquitin Binding Entities (TUBEs). SLAS Discov 2020; 25:350-360. [PMID: 31997692 DOI: 10.1177/2472555219901261] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Protein turnover is highly regulated by the posttranslational process of ubiquitination. Deregulation of the ubiquitin proteasome system (UPS) has been implicated in cancer and neurodegenerative diseases, and modulating this system has proven to be a viable approach for therapeutic intervention. The development of novel technologies that enable high-throughput studies of substrate protein ubiquitination is key for UPS drug discovery. Conventional approaches for studying ubiquitination either have high protein requirements or rely on exogenous or modified ubiquitin moieties, thus limiting their utility. In order to circumvent these issues, we developed a high-throughput live-cell assay that combines the NanoBiT luminescence-based technology with tandem ubiquitin binding entities (TUBEs) to resolve substrate ubiquitination. To demonstrate the effectiveness and utility of this assay, we studied compound-induced ubiquitination of the G to S Phase Transition 1 (GSPT1) protein. Using this assay, we characterized compounds with varying levels of GSPT1 ubiquitination activity. This method provides a live-cell-based approach for assaying substrate ubiquitination that can be adapted to study the kinetics of ubiquitin transfer onto a substrate protein of interest. In addition, our results show that this approach is portable for studying the ubiquitination of target proteins with diverse functions.
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Affiliation(s)
- Favour A Akinjiyan
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Aleem Fazal
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Marc Hild
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Rohan E J Beckwith
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Nathan T Ross
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Joshiawa Paulk
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Seth Carbonneau
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
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12
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Pashikanti S, Afrin F, Meldrum TC, Stegelmeier JL, Pavek A, Habashi YA, Fatema K, Barrott JJ. Quantifying Fluorescently Labeled Ceramide Levels in Human Sarcoma Cell Lines in Response to a Sphingomyelin Synthase Inhibitor. Methods Protoc 2019; 2:mps2030076. [PMID: 31480447 PMCID: PMC6789850 DOI: 10.3390/mps2030076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 08/12/2019] [Accepted: 08/29/2019] [Indexed: 12/15/2022] Open
Abstract
Sphingolipid metabolism is an important process in sustaining the growth needs of rapidly dividing cancer cells. Enzymes that synthesize sphingolipids have become attractive targets in cancer pharmacology. Ceramide is a precursor for synthesizing sphingolipids such as sphingomyelin, sphingosine-1-phosphate, and glucosylceramide. Sphingomyelin synthase (SMS) is the enzyme that transfers a phosphatidylcholine to ceramide to generate sphingomyelin. To test the inhibition of SMS, scientists assess the buildup of ceramide in the cell, which is cytotoxic. Because ceramide is a small lipid molecule, there are limited tools like antibodies to detect its presence. Alternatively, designated machines for small-molecule separation coupled with mass spectrometry detection can be used; however, these can be cost-prohibitive. We used a commercially available NBD-ceramide to apply to human cancer cell lines in the presence or absence of a known SMS inhibitor, jaspine B. After short incubation times, we were able to collect cell lysates and using solvent extraction methods, run the cellular material on a thin-layer chromatography plate to determine the levels of intact fluorescently labeled ceramide. Brighter fluorescence on the TLC plate correlated to greater SMS inhibition. Small molecules can then be screened quantifiably to determine the biological impact of inhibiting the sphingolipid metabolism pathways involving ceramide.
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Affiliation(s)
- Srinath Pashikanti
- Department of Biomedical and Pharmaceutical Sciences, Idaho State University, Pocatello, ID 83209, USA
| | - Farjana Afrin
- Department of Biomedical and Pharmaceutical Sciences, Idaho State University, Pocatello, ID 83209, USA
| | - Trevor C Meldrum
- Department of Biomedical and Pharmaceutical Sciences, Idaho State University, Pocatello, ID 83209, USA
| | - John L Stegelmeier
- Department of Biomedical and Pharmaceutical Sciences, Idaho State University, Pocatello, ID 83209, USA
| | - Adriene Pavek
- Department of Biomedical and Pharmaceutical Sciences, Idaho State University, Pocatello, ID 83209, USA
| | - Yashar A Habashi
- Department of Biomedical and Pharmaceutical Sciences, Idaho State University, Pocatello, ID 83209, USA
| | - Kaniz Fatema
- Department of Biomedical and Pharmaceutical Sciences, Idaho State University, Pocatello, ID 83209, USA
| | - Jared J Barrott
- Department of Biomedical and Pharmaceutical Sciences, Idaho State University, Pocatello, ID 83209, USA.
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13
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Zand Z, Khaki PA, Salihi A, Sharifi M, Qadir Nanakali NM, Alasady AA, Aziz FM, Shahpasand K, Hasan A, Falahati M. Cerium oxide NPs mitigate the amyloid formation of α-synuclein and associated cytotoxicity. Int J Nanomedicine 2019; 14:6989-7000. [PMID: 31695369 PMCID: PMC6718255 DOI: 10.2147/ijn.s220380] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 08/09/2019] [Indexed: 12/15/2022] Open
Abstract
Aim Among therapeutic proposals for amyloid-associated disorders, special attention has been given to the exploitation of nanoparticles (NPs) as promising agents against aggregation. Methods In this paper, the inhibitory effect of cerium oxide (CeO2) NPs against α-synuclein (α-syn) amyloid formation was explored by different methods such as Thioflavin T (ThT) and 8-anilinonaphthalene-1-sulfonic acid (ANS) fluorescence spectroscopy, Congo red adsorption assay, circular dichroism (CD) spectroscopy, transmission electron microscopy (TEM), and bioinformatical approaches. Also, the cytotoxicity of α-syn amyloid either alone or with CeO2 NPs against neuron-like cells (SH-SY5Y) was examined using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT), flow cytometry, and quantitative real-time polymerase chain reaction (Bax and Bcl-2 gene expression) assays. Results ThT and ANS fluorescence assays indicated that CeO2 NPs inhibit the formation of aggregated species and hydrophobic patches of α-syn in amyloidogenic conditions, respectively. Congo red and CD assays demonstrated that CeO2 NPs reduce the formation of amyloid species and β-sheets structures of α-syn molecules, respectively. TEM investigation also confirmed that CeO2 NPs limited the formation of well-defined fibrillary structures of α-syn molecules. Molecular docking and dynamic studies revealed that CeO2 NPs could bind with different affinities to α-syn monomer and amyloid species and fibrillar structure of α-syn is disaggregated in the presence of CeO2 NPs. Moreover, cellular assays depicted that CeO2 NPs mitigate the cell mortality, apoptosis, and the ratio of Bax/Bcl-2 gene expression associated with α-syn amyloids. Conclusion It may be concluded that CeO2 NPs can be used as therapeutic agents to reduce the aggregation of proteins and mitigate the occurrence of neurodegenerative diseases.
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Affiliation(s)
- Zahra Zand
- Department of Biochemistry and Biophysics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Pegah Afarinesh Khaki
- Department of Molecular Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Abbas Salihi
- Department of Biology, College of Science, Salahaddin University-Erbil, Kurdistan Region, Iraq.,Department of Medical Analysis, Faculty of Science, Tishk International University, Erbil, Iraq
| | - Majid Sharifi
- Department of Nanomedicine, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.,Department of Animal Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| | - Nadir Mustafa Qadir Nanakali
- Department of Biology, College of Science, Cihan University-Erbil, Kurdistan Region, Iraq.,Department of Biology, College of Education, Salahaddin University-Erbil, Kurdistan Region, Iraq
| | - Asaad Ab Alasady
- Anatomy, Biology and Histology Unit, College of Medicine, University of Duhok, Kurdistan Region, Iraq
| | - Falah Mohammad Aziz
- Department of Biology, College of Science, Salahaddin University-Erbil, Kurdistan Region, Iraq
| | - Koorosh Shahpasand
- Department of Brain and Cognitive Sciences, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Anwarul Hasan
- Department of Mechanical and Industrial Engineering, College of Engineering, Qatar University, Doha 2713, Qatar.,Biomedical Research Center, Qatar University, Doha 2713, Qatar
| | - Mojtaba Falahati
- Department of Nanomedicine, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
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14
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da S M Forezi L, Froes TQ, Cardoso MFC, de Oliveira Maciel CA, Nicastro GG, Baldini RL, Costa DCS, Ferreira VF, Castilho MS, de C da Silva F. Synthesis and Biological Evaluation of Coumarins Derivatives as Potential Inhibitors of the Production of Pseudomonas aeruginosa Virulence Factor Pyocyanin. Curr Top Med Chem 2018; 18:149-156. [PMID: 29595112 DOI: 10.2174/1568026618666180329122704] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 02/02/2018] [Accepted: 03/05/2018] [Indexed: 11/22/2022]
Abstract
Antimicrobial Resistance (AMR) is a serious problem for the humans since it threatens the effective prevention and treatment of an ever-increasing range of infections caused by bacteria, parasites, viruses and fungi. One way around this problem is to act on the virulence factors, produced by bacteria, which increase their infection effectiveness. In view of these facts, new coumarin derivatives were synthesized and evaluated for their anti-virulence biological activity towards Pseudomonas aeruginosa. The results suggest that coumarin derivatives with a secondary carbon at C-3 position reduces P. aeruginosa growth whereas compounds with one additional substituent have a significant effect over pyocyanin production (10k EC50 7 ± 2 µM; 10l EC50 42 ± 13 µM). Moreover, 10k reduces P. aeruginosa motility and biofilm formation, what is compatible with a quorum sensing related mechanism of action.
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Affiliation(s)
- Luana da S M Forezi
- Departamento de Quimica Organica, Universidade Federal Fluminense, Instituto de Quimica, Niteroi, RJ, 24020-150, Brazil
| | - Thamires Quadros Froes
- Programa de pos-graduacao em Biotecnologia da Universidade Estadual de Feira de Santana, Feira de Santana, BA, Brazil.,Faculdade de Farmácia da Universidade Federal da Bahia, Bahia, Salvador, BA, Brazil
| | - Mariana F C Cardoso
- Departamento de Quimica Organica, Universidade Federal Fluminense, Instituto de Quimica, Niteroi, RJ, 24020-150, Brazil
| | - Carine Assuncao de Oliveira Maciel
- Programa de pos-graduacao em Biotecnologia da Universidade Estadual de Feira de Santana, Feira de Santana, BA, Brazil.,Faculdade de Farmácia da Universidade Federal da Bahia, Bahia, Salvador, BA, Brazil
| | - Gianluca G Nicastro
- Departamento de Bioquimica, Instituto de Quimica, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Regina L Baldini
- Departamento de Bioquimica, Instituto de Quimica, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Dora C S Costa
- Departamento de Quimica Organica, Universidade Federal Fluminense, Instituto de Quimica, Niteroi, RJ, 24020-150, Brazil
| | - Vitor F Ferreira
- Universidade Federal Fluminense, Departamento de Tecnologia Farmaceutica, Faculdade de Farmacia, Niteroi, RJ, 24241-002, Brazil
| | - Marcelo S Castilho
- Departamento de Quimica Organica, Universidade Federal Fluminense, Instituto de Quimica, Niteroi, RJ, 24020-150, Brazil.,Programa de pos-graduacao em Biotecnologia da Universidade Estadual de Feira de Santana, Feira de Santana, BA, Brazil
| | - Fernando de C da Silva
- Departamento de Quimica Organica, Universidade Federal Fluminense, Instituto de Quimica, Niteroi, RJ, 24020-150, Brazil
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15
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Ng PKS, Li J, Jeong KJ, Shao S, Chen H, Tsang YH, Sengupta S, Wang Z, Bhavana VH, Tran R, Soewito S, Minussi DC, Moreno D, Kong K, Dogruluk T, Lu H, Gao J, Tokheim C, Zhou DC, Johnson AM, Zeng J, Ip CKM, Ju Z, Wester M, Yu S, Li Y, Vellano CP, Schultz N, Karchin R, Ding L, Lu Y, Cheung LWT, Chen K, Shaw KR, Meric-Bernstam F, Scott KL, Yi S, Sahni N, Liang H, Mills GB. Systematic Functional Annotation of Somatic Mutations in Cancer. Cancer Cell 2018; 33:450-462.e10. [PMID: 29533785 PMCID: PMC5926201 DOI: 10.1016/j.ccell.2018.01.021] [Citation(s) in RCA: 163] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 12/07/2017] [Accepted: 01/30/2018] [Indexed: 12/11/2022]
Abstract
The functional impact of the vast majority of cancer somatic mutations remains unknown, representing a critical knowledge gap for implementing precision oncology. Here, we report the development of a moderate-throughput functional genomic platform consisting of efficient mutant generation, sensitive viability assays using two growth factor-dependent cell models, and functional proteomic profiling of signaling effects for select aberrations. We apply the platform to annotate >1,000 genomic aberrations, including gene amplifications, point mutations, indels, and gene fusions, potentially doubling the number of driver mutations characterized in clinically actionable genes. Further, the platform is sufficiently sensitive to identify weak drivers. Our data are accessible through a user-friendly, public data portal. Our study will facilitate biomarker discovery, prediction algorithm improvement, and drug development.
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Affiliation(s)
- Patrick Kwok-Shing Ng
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jun Li
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kang Jin Jeong
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Shan Shao
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hu Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yiu Huen Tsang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sohini Sengupta
- Division of Oncology, Department of Medicine, Washington University, St. Louis, MO 63108, USA
| | - Zixing Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | | | - Richard Tran
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Stephanie Soewito
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Darlan Conterno Minussi
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Daniela Moreno
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kathleen Kong
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Turgut Dogruluk
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hengyu Lu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jianjiong Gao
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Collin Tokheim
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA; Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Daniel Cui Zhou
- Division of Oncology, Department of Medicine, Washington University, St. Louis, MO 63108, USA
| | - Amber M Johnson
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jia Zeng
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Carman Ka Man Ip
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Zhenlin Ju
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Matthew Wester
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Shuangxing Yu
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yongsheng Li
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Christopher P Vellano
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Nikolaus Schultz
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Rachel Karchin
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA; Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218, USA; Department of Oncology, Johns Hopkins Medicine, Baltimore, MD 21287, USA
| | - Li Ding
- Division of Oncology, Department of Medicine, Washington University, St. Louis, MO 63108, USA; Siteman Cancer Center, Washington University, St. Louis, MO 63108, USA
| | - Yiling Lu
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lydia Wai Ting Cheung
- HKU Shenzhen Institute of Research and Innovation, Shenzhen, China; School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kenna R Shaw
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Funda Meric-Bernstam
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Breast Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kenneth L Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Song Yi
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Nidhi Sahni
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Han Liang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Gordon B Mills
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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16
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Verhoef LGGC, Wade M. Visualization of Protein Interactions in Living Cells Using Bimolecular Luminescence Complementation (BiLC). ACTA ACUST UNITED AC 2017; 90:30.5.1-30.5.14. [PMID: 29091275 DOI: 10.1002/cpps.42] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The number of intracellular protein-protein interactions (PPIs) far exceeds the total number of proteins encoded by the genome. Dynamic cellular PPI networks respond to external stimuli and endogenous metabolism in order to maintain homeostasis. Many PPIs are directly involved in disease pathogenesis and/or resistance to therapeutics; they therefore represent potential drug targets. A technology generally termed 'bimolecular complementation' relies on the physical splitting of a molecular reporter (such as a fluorescent or luminescent protein) and fusion of the resulting two fragments to a pair of interacting proteins. When these proteins interact, they effectively reconstitute the activity of the molecular reporter (typically leading to increased fluorescence or luminescence). This unit describes the selection and development of bimolecular luminescence complementation (BiLC) assays for reporting intracellular PPIs, and provides examples in which BiLC was used to identify small molecules that can modulate PPIs. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Lisette G G C Verhoef
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, Milan, Italy
| | - Mark Wade
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, Milan, Italy
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17
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Leba LJ, Brunschwig C, Saout M, Martial K, Bereau D, Robinson JC. Oenocarpus bacaba and Oenocarpus bataua Leaflets and Roots: A New Source of Antioxidant Compounds. Int J Mol Sci 2016; 17:E1014. [PMID: 27355943 DOI: 10.3390/ijms17071014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 06/17/2016] [Accepted: 06/20/2016] [Indexed: 12/15/2022] Open
Abstract
Native palm trees fruit from the Amazonian rainforest, Oenocarpus bacaba and Oenocarpus bataua, are very often used in the diet of local communities, but the biological activities of their roots and leaflets remain poorly known. Total phenolic content (TPC) and antioxidant activity of root and leaflet extracts from Oenocarpus bacaba and Oenocarpus bataua were assessed by using different chemical assays, the oxygèn radical absorbance capacity (ORAC), the 2,2-diphenyl-l-picrylhydrazyl (DPPH) free radical-scavenging capacity and the ferric-reducing ability of plasma (FRAP). Cellular antioxidant activity and cytotoxicity were also measured in Normal Human Dermal Fibroblasts. The polyphenolic composition of Oenocarpus extracts was investigated by LC-MSn. Oenocarpus leaflet extracts were more antioxidant than root extracts, being at least as potent as Euterpe oleracea berries known as superfruit. Oenocarpus root extracts were characterized by hydroxycinnamic acids (caffeoylquinic and caffeoylshikimic acids), while leaflet extracts contained mainly caffeoylquinic acids and C-glycosyl flavones. These results suggest that leaflets of both Oenocarpus species could be valorized as a new non-cytotoxic source of antioxidants from Amazonia, containing hydroxycinnamic acids and flavonoids, in the pharmaceutical, cosmetic or agri-food industry.
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18
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Das RK, Brar SK, Verma M. Checking the Biocompatibility of Plant-Derived Metallic Nanoparticles: Molecular Perspectives. Trends Biotechnol 2016; 34:440-449. [PMID: 26948438 DOI: 10.1016/j.tibtech.2016.02.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2015] [Revised: 02/04/2016] [Accepted: 02/05/2016] [Indexed: 11/16/2022]
Abstract
Understanding the biocompatibility of metallic nanoparticles (MNPs) is pivotal for biomedical applications. The biocompatibility of plant-derived MNPs has been mostly attributed to capped plant molecules. This claim seems to be straightforward but lacks conclusive evidence. The capped phytochemicals and the metallic core might have decisive and individual roles in imparting the overall biocompatibility. Whether capped phytochemicals really make sense in diminishing the toxicity effect of the otherwise naked or metallic core needs further analysis. Here, we readdress the biocompatibility of plant-derived MNPs with references to contemporary cellular assays, different reactants for green synthesis, possible epigenetic involvement, and nanobiocompatibility at the molecular level. Finally, we discuss relevant in vivo studies and large-scale production issues.
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Affiliation(s)
- Ratul Kumar Das
- ETE Centre, INRS Université, 490, Rue de la Couronne, Québec, QC, G1K 9A9, Canada
| | - Satinder Kaur Brar
- ETE Centre, INRS Université, 490, Rue de la Couronne, Québec, QC, G1K 9A9, Canada.
| | - Mausam Verma
- CO(2) Solutions Inc., 2300, rue Jean-Perrin, Québec, QC, G2C 1T9, Canada
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Mata-Cantero L, Cid C, Gomez-Lorenzo MG, Xolalpa W, Aillet F, Martín JJ, Rodriguez MS. Development of two novel high-throughput assays to quantify ubiquitylated proteins in cell lysates: application to screening of new anti-malarials. Malar J 2015; 14:200. [PMID: 25968882 PMCID: PMC4440562 DOI: 10.1186/s12936-015-0708-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 04/20/2015] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND The ubiquitin proteasome system (UPS) is one of the main proteolytical pathways in eukaryotic cells and plays an essential role in key cellular processes such as cell cycle, stress response, signal transduction, and transcriptional regulation. Many components of this pathway have been implicated in diverse pathologies including cancer, neurodegeneration and infectious diseases, such as malaria. The success of proteasome inhibitors in clinical trials underlines the potential of the UPS in drug discovery. METHODS Plasmodium falciparum, the malaria causative pathogen, has been used to develop two assays that allow the quantification of the parasite protein ubiquitylation levels in a high-throughput format that can be used to find new UPS inhibitors. RESULTS In both assays tandem ubiquitin binding entities (TUBEs), also known as ubiquitin traps, have been used to capture ubiquitylated proteins from cell lysates. The primary assay is based on AlphaLISA technology, and the orthogonal secondary assay relies on a dissociation-enhanced lanthanide fluorescent immunoassay (DELFIA) system. A panel of well-known proteasome inhibitors has been used to validate both technologies. An excellent correlation was obtained between these biochemical assays and the standard whole cell assay that measures parasite growth inhibition. CONCLUSIONS The two assays presented can be used in a high-throughput format to find new UPS inhibitors for P. falciparum and could help to identify new targets within this system. This methodology is also applicable to other cellular contexts or pathologies.
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Affiliation(s)
- Lydia Mata-Cantero
- Present address: Tres Cantos Medicines Development Campus, Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, 28760, , Madrid, Spain.
- Centro de Investigación Básica, GlaxoSmithKline, Santiago Grisolía 4, 28760, Tres Cantos, Madrid, Spain.
- Ubiquitylation and Cancer Molecular Biology, Inbiomed, Mikeletegi 81, 20009, San Sebastian, Spain.
| | - Concepción Cid
- Centro de Investigación Básica, GlaxoSmithKline, Santiago Grisolía 4, 28760, Tres Cantos, Madrid, Spain.
| | - Maria G Gomez-Lorenzo
- Present address: Tres Cantos Medicines Development Campus, Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, 28760, , Madrid, Spain.
| | - Wendy Xolalpa
- Ubiquitylation and Cancer Molecular Biology, Inbiomed, Mikeletegi 81, 20009, San Sebastian, Spain.
| | - Fabienne Aillet
- Ubiquitylation and Cancer Molecular Biology, Inbiomed, Mikeletegi 81, 20009, San Sebastian, Spain.
| | - J Julio Martín
- Centro de Investigación Básica, GlaxoSmithKline, Santiago Grisolía 4, 28760, Tres Cantos, Madrid, Spain.
| | - Manuel S Rodriguez
- Ubiquitylation and Cancer Molecular Biology, Inbiomed, Mikeletegi 81, 20009, San Sebastian, Spain.
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20
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Bier C, Knauer SK, Klapthor A, Schweitzer A, Rekik A, Krämer OH, Marschalek R, Stauber RH. Cell-based analysis of structure-function activity of threonine aspartase 1. J Biol Chem 2011; 286:3007-17. [PMID: 21084304 PMCID: PMC3024795 DOI: 10.1074/jbc.m110.161646] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2010] [Revised: 10/22/2010] [Indexed: 12/24/2022] Open
Abstract
Taspase1 is a threonine protease responsible for cleaving intracellular substrates. As such, (de)regulated Taspase1 function is expected not only to be vital for ordered development but may also be relevant for disease. However, the full repertoires of Taspase1 targets as well as the exact biochemical requirements for its efficient and substrate-specific cleavage are not yet resolved. Also, no cellular assays for this protease are currently available, hampering the exploitation of the (patho)biological relevance of Taspase1. Here, we developed highly efficient cell-based translocation biosensor assays to probe Taspase1 trans-cleavage in vivo. These modular sensors harbor variations of Taspase1 cleavage sites and localize to the cytoplasm. Expression of Taspase1 but not of inactive Taspase1 mutants or of unrelated proteases triggers proteolytic cleavage and nuclear accumulation of the biosensors. Employing our assay combined with scanning mutagenesis, we identified the sequence and spatial requirements for efficient Taspase1 processing in liquid and solid tumor cell lines. Collectively, our results defined an improved Taspase1 consensus recognition sequence, Q(3)(F/I/L/V)(2)D(1)↓G(1)'X(2)'D(3)'D(4)', allowing the first genome-wide bioinformatic identification of the human Taspase1 degradome. Among the 27 most likely Taspase1 targets are cytoplasmic but also nuclear proteins, such as the upstream stimulatory factor 2 (USF2) or the nuclear RNA export factors 2/5 (NXF2/5). Cleavage site recognition and proteolytic processing of selected targets were verified in the context of the biosensor and for the full-length proteins. We provide novel mechanistic insights into the function and bona fide targets of Taspase1 allowing for a focused investigation of the (patho)biological relevance of this type 2 asparaginase.
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Affiliation(s)
- Carolin Bier
- From the Molecular and Cellular Oncology/Mainzer Screening Center, University Hospital of Mainz, Langenbeckstrasse 1, 55101 Mainz
| | - Shirley K. Knauer
- the Institute for Molecular Biology, Centre for Medical Biotechnology, University Duisburg-Essen, Universitätsstrasse, 45117 Essen
| | - Alexander Klapthor
- From the Molecular and Cellular Oncology/Mainzer Screening Center, University Hospital of Mainz, Langenbeckstrasse 1, 55101 Mainz
| | - Andrea Schweitzer
- From the Molecular and Cellular Oncology/Mainzer Screening Center, University Hospital of Mainz, Langenbeckstrasse 1, 55101 Mainz
| | - Alexander Rekik
- From the Molecular and Cellular Oncology/Mainzer Screening Center, University Hospital of Mainz, Langenbeckstrasse 1, 55101 Mainz
| | - Oliver H. Krämer
- the Institute for Biochemistry and Biophysics/Centre for Molecular Biomedicine, Friedrich-Schiller-University Jena, Hans-Knöll-Strasse 2, 07745 Jena, and
| | - Rolf Marschalek
- the Institute for Pharmaceutical Biology/ZAFES, Goethe-University, Max-von Laue-Strasse 9, 60438 Frankfurt/Main, Germany
| | - Roland H. Stauber
- From the Molecular and Cellular Oncology/Mainzer Screening Center, University Hospital of Mainz, Langenbeckstrasse 1, 55101 Mainz
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21
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Ingham CJ, Sprenkels A, Bomer J, Molenaar D, van den Berg A, van Hylckama Vlieg JET, de Vos WM. The micro-Petri dish, a million-well growth chip for the culture and high-throughput screening of microorganisms. Proc Natl Acad Sci U S A 2007; 104:18217-22. [PMID: 17989237 PMCID: PMC2084323 DOI: 10.1073/pnas.0701693104] [Citation(s) in RCA: 204] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2007] [Indexed: 11/18/2022] Open
Abstract
A miniaturized, disposable microbial culture chip has been fabricated by microengineering a highly porous ceramic sheet with up to one million growth compartments. This versatile culture format, with discrete compartments as small as 7 x 7 mum, allowed the growth of segregated microbial samples at an unprecedented density. The chip has been used for four complementary applications in microbiology. (i) As a fast viable counting system that showed a dynamic range of over 10,000, a low degree of bias, and a high culturing efficiency. (ii) In high-throughput screening, with the recovery of 1 fluorescent microcolony in 10,000. (iii) In screening for an enzyme-based, nondominant phenotype by the targeted recovery of Escherichia coli transformed with the plasmid pUC18, based on expression of the lacZ reporter gene without antibiotic-resistance selection. The ease of rapid, successive changes in the environment of the organisms on the chip, needed for detection of beta-galactosidase activity, highlights an advantageous feature that was also used to screen a metagenomic library for the same activity. (iv) In high-throughput screening of >200,000 isolates from Rhine water based on metabolism of a fluorogenic organophosphate compound, resulting in the recovery of 22 microcolonies with the desired phenotype. These isolates were predicted, on the basis of rRNA sequence, to include six new species. These four applications suggest that the potential for such simple, readily manufactured chips to impact microbial culture is extensive and may facilitate the full automation and multiplexing of microbial culturing, screening, counting, and selection.
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Affiliation(s)
- Colin J Ingham
- Top Institute Food and Nutrition, 6703 CT, Wageningen, The Netherlands.
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