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Gilbert DF, Friedrich O, Wiest J. Assaying Proliferation Characteristics of Cells Cultured Under Static Versus Periodic Conditions. Methods Mol Biol 2023; 2644:35-45. [PMID: 37142914 DOI: 10.1007/978-1-0716-3052-5_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Two-dimensional in vitro culture models are widely being employed for assessing a vast variety of biological questions in different scientific fields. Common in vitro culture models are typically maintained under static conditions, where the surrounding culture medium is replaced every few days-typically every 48 to 72 h-with the aim to remove metabolites and to replenish nutrients. Although this approach is sufficient for supporting cellular survival and proliferation, static culture conditions do mostly not reflect the in vivo situation where cells are continuously being perfused by extracellular fluid, and thus, create a less-physiological environment. In order to evaluate whether the proliferation characteristics of cells in 2D culture maintained under static conditions differ from cells kept in a dynamic environment, in this chapter, we provide a protocol for differential analysis of cellular growth under static versus pulsed-perfused conditions, mimicking continuous replacement of extracellular fluid in the physiological environment. The protocol involves long-term life-cell high-content time-lapse imaging of fluorescent cells at 37 °C and ambient CO2 concentration using multi-parametric biochips applicable for microphysiological analysis of cellular vitality. We provide instructions and useful information for (i) the culturing of cells in biochips, (ii) setup of cell-laden biochips for culturing cells under static and pulsed-perfused conditions, (iii) long-term life-cell high-content time-lapse imaging of fluorescent cells in biochips, and (iv) quantification of cellular proliferation from image series generated from imaging of differentially cultured cells.
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Affiliation(s)
- Daniel F Gilbert
- Institute of Medical Biotechnology, Department of Chemical and Biological Engineering (CBI), Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany.
| | - Oliver Friedrich
- Institute of Medical Biotechnology, Department of Chemical and Biological Engineering (CBI), Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
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Zimoń M, Huang Y, Trasta A, Halavatyi A, Liu JZ, Chen CY, Blattmann P, Klaus B, Whelan CD, Sexton D, John S, Huber W, Tsai EA, Pepperkok R, Runz H. Pairwise effects between lipid GWAS genes modulate lipid plasma levels and cellular uptake. Nat Commun 2021; 12:6411. [PMID: 34741066 PMCID: PMC8571362 DOI: 10.1038/s41467-021-26761-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 10/09/2021] [Indexed: 12/27/2022] Open
Abstract
Complex traits are characterized by multiple genes and variants acting simultaneously on a phenotype. However, studying the contribution of individual pairs of genes to complex traits has been challenging since human genetics necessitates very large population sizes, while findings from model systems do not always translate to humans. Here, we combine genetics with combinatorial RNAi (coRNAi) to systematically test for pairwise additive effects (AEs) and genetic interactions (GIs) between 30 lipid genome-wide association studies (GWAS) genes. Gene-based burden tests from 240,970 exomes show that in carriers with truncating mutations in both, APOB and either PCSK9 or LPL ("human double knock-outs") plasma lipid levels change additively. Genetics and coRNAi identify overlapping AEs for 12 additional gene pairs. Overlapping GIs are observed for TOMM40/APOE with SORT1 and NCAN. Our study identifies distinct gene pairs that modulate plasma and cellular lipid levels primarily via AEs and nominates putative drug target pairs for improved lipid-lowering combination therapies.
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Affiliation(s)
- Magdalena Zimoń
- grid.4709.a0000 0004 0495 846XMolecular Medicine Partnership Unit (MMPU), University of Heidelberg/EMBL, Heidelberg, Germany ,Cell Biology and Biophysics Unit, European Molecular Biological Laboratory, Heidelberg, Germany
| | - Yunfeng Huang
- grid.417832.b0000 0004 0384 8146Translational Biology, Biogen Inc, Cambridge, MA USA
| | - Anthi Trasta
- grid.4709.a0000 0004 0495 846XMolecular Medicine Partnership Unit (MMPU), University of Heidelberg/EMBL, Heidelberg, Germany ,Cell Biology and Biophysics Unit, European Molecular Biological Laboratory, Heidelberg, Germany
| | - Aliaksandr Halavatyi
- Advanced Light Microscopy Facility (ALMF), European Molecular Biological Laboratory, Heidelberg, Germany
| | - Jimmy Z. Liu
- grid.417832.b0000 0004 0384 8146Translational Biology, Biogen Inc, Cambridge, MA USA
| | - Chia-Yen Chen
- grid.417832.b0000 0004 0384 8146Translational Biology, Biogen Inc, Cambridge, MA USA ,grid.32224.350000 0004 0386 9924Psychiatric and Neurodevelopmental Genetics Unit, Mass General Hospital, Boston, MA USA
| | - Peter Blattmann
- grid.4709.a0000 0004 0495 846XMolecular Medicine Partnership Unit (MMPU), University of Heidelberg/EMBL, Heidelberg, Germany ,Cell Biology and Biophysics Unit, European Molecular Biological Laboratory, Heidelberg, Germany ,grid.508389.f0000 0004 6414 2411Idorsia Pharmaceuticals Ltd, Basel, Switzerland
| | - Bernd Klaus
- Genome Biology Unit, European Molecular Biological Laboratory, Heidelberg, Germany
| | - Christopher D. Whelan
- grid.417832.b0000 0004 0384 8146Translational Biology, Biogen Inc, Cambridge, MA USA
| | - David Sexton
- grid.417832.b0000 0004 0384 8146Translational Biology, Biogen Inc, Cambridge, MA USA
| | - Sally John
- grid.417832.b0000 0004 0384 8146Translational Biology, Biogen Inc, Cambridge, MA USA
| | - Wolfgang Huber
- Genome Biology Unit, European Molecular Biological Laboratory, Heidelberg, Germany
| | - Ellen A. Tsai
- grid.417832.b0000 0004 0384 8146Translational Biology, Biogen Inc, Cambridge, MA USA
| | - Rainer Pepperkok
- grid.4709.a0000 0004 0495 846XMolecular Medicine Partnership Unit (MMPU), University of Heidelberg/EMBL, Heidelberg, Germany ,Cell Biology and Biophysics Unit, European Molecular Biological Laboratory, Heidelberg, Germany ,Advanced Light Microscopy Facility (ALMF), European Molecular Biological Laboratory, Heidelberg, Germany
| | - Heiko Runz
- grid.4709.a0000 0004 0495 846XMolecular Medicine Partnership Unit (MMPU), University of Heidelberg/EMBL, Heidelberg, Germany ,grid.417832.b0000 0004 0384 8146Translational Biology, Biogen Inc, Cambridge, MA USA
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3
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Carullo G, Mazzotta S, Koch A, Hartmann KM, Friedrich O, Gilbert DF, Vega-Holm M, Schneider-Stock R, Aiello F. New Oleoyl Hybrids of Natural Antioxidants: Synthesis and In Vitro Evaluation as Inducers of Apoptosis in Colorectal Cancer Cells. Antioxidants (Basel) 2020; 9:antiox9111077. [PMID: 33153029 PMCID: PMC7692320 DOI: 10.3390/antiox9111077] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 10/27/2020] [Accepted: 10/30/2020] [Indexed: 12/13/2022] Open
Abstract
Nowadays, the beneficial role of a healthy lifestyle, particularly emphasizing the quality of foods and cancer management, is accepted worldwide. Polyphenols and oleic acid play a key role in this context, but are still scarcely used as anti-cancer agents due to their bio-accessibility limits. Therefore, we aimed to synthesize a set of new oleoyl-hybrids of quercetin, morin, pinocembrin, and catechin to overcome the low bioavailability of polyphenols, throughout a bio-catalytic approach using pancreatic porcine lipase as a catalyst. The in vitro assays, using a wide panel of human cancer cell lines showed, mainly for two novel regioisomer oleoyl-hybrids of quercetin, a remarkable increase in apoptotic cell populations. We suggested that the DNA damage shown as ɣH2AX signals might be the major cause of apoptotic cell death. Finally, we demonstrated convincing data about two novel polyphenol-based hybrids displaying a highly selective anti-cancer cytotoxicity and being superior compared to their reference/parental compounds.
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Affiliation(s)
- Gabriele Carullo
- Department of Biotechnology, Chemistry and Pharmacy, Department of Excellence 2018-2022, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy;
- Department of Pharmacy, Health and Nutritional Sciences, Department of Excellence 2018-2022, University of Calabria, Edificio Polifunzionale, 87036 Rende (CS), Italy
| | - Sarah Mazzotta
- Department of Pharmacy, Health and Nutritional Sciences, Department of Excellence 2018-2022, University of Calabria, Edificio Polifunzionale, 87036 Rende (CS), Italy
- Department of Pharmaceutical Sciences, University of Milan Via Luigi Mangiagalli 25, 20133 Milano, Italy;
- Department of Organic and Medicinal Chemistry, Faculty of Pharmacy, University of Seville, Profesor García González 2, 41071 Seville, Spain;
| | - Adrian Koch
- Institiute of Pathology, University Hospital, Friedrich-Alexander University Erlangen-Nürnberg Universitätsstr. 22, 91054 Erlangen, Germany;
- Experimental Tumorpathology, University Hospital, Friedrich-Alexander University Erlangen-Nürnberg Universitätsstr. 22, 91054 Erlangen, Germany
| | - Kristin M. Hartmann
- Institute of Medical Biotechnology Friedrich-Alexander-University Erlangen-Nürnberg, Paul-Gordan-Str. 3, 91052 Erlangen, Germany; (K.M.H.); (O.F.); (D.F.G.)
- Erlangen Graduate School in Advanced Optical Technologies (SAOT), Friedrich-Alexander-University Erlangen-Nürnberg, Paul-Gordan-Str. 6, 91052 Erlangen, Germany
| | - Oliver Friedrich
- Institute of Medical Biotechnology Friedrich-Alexander-University Erlangen-Nürnberg, Paul-Gordan-Str. 3, 91052 Erlangen, Germany; (K.M.H.); (O.F.); (D.F.G.)
| | - Daniel F. Gilbert
- Institute of Medical Biotechnology Friedrich-Alexander-University Erlangen-Nürnberg, Paul-Gordan-Str. 3, 91052 Erlangen, Germany; (K.M.H.); (O.F.); (D.F.G.)
| | - Margarita Vega-Holm
- Department of Organic and Medicinal Chemistry, Faculty of Pharmacy, University of Seville, Profesor García González 2, 41071 Seville, Spain;
| | - Regine Schneider-Stock
- Institiute of Pathology, University Hospital, Friedrich-Alexander University Erlangen-Nürnberg Universitätsstr. 22, 91054 Erlangen, Germany;
- Experimental Tumorpathology, University Hospital, Friedrich-Alexander University Erlangen-Nürnberg Universitätsstr. 22, 91054 Erlangen, Germany
- Correspondence: (R.S.-S.); (F.A.)
| | - Francesca Aiello
- Department of Pharmacy, Health and Nutritional Sciences, Department of Excellence 2018-2022, University of Calabria, Edificio Polifunzionale, 87036 Rende (CS), Italy
- Correspondence: (R.S.-S.); (F.A.)
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Ritter P, Bye LJ, Finol-Urdaneta RK, Lesko C, Adams DJ, Friedrich O, Gilbert DF. A method for high-content functional imaging of intracellular calcium responses in gelatin-immobilized non-adherent cells. Exp Cell Res 2020; 395:112210. [PMID: 32750330 DOI: 10.1016/j.yexcr.2020.112210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 07/15/2020] [Accepted: 07/28/2020] [Indexed: 11/28/2022]
Abstract
Functional imaging of the intracellular calcium concentration [Ca2+]i using fluorescent indicators is a powerful and frequently applied method for assessing various biological questions in vitro, including ion channel function and intracellular signaling in homeostasis and disease. In functional [Ca2+]i imaging experiments, the fluorescence intensity of single cells is typically recorded during application of a chemical stimulus, i.e. by exchange of modified extracellular media, exposure to drugs and/or ligands. The concomitant mechanical perturbation caused by the perfusion of different solution during experimentation severely hinders calcium imaging in non-adherent cells, including peripheral immune cells, as cells in suspension are dislocated by turbulent flow during chemical stimulation. The quantitative analysis, involving time-courses of intracellular fluorescence signal changes, necessitates cells to remain at the same position throughout the experiment. To prevent dislocation of cells during solution exchange, and to enable imaging as well as analysis of Ca2+ responses in immune cells, a gelatin-based method for immobilization of non-adherent cells was developed. Gelatin has been a long-serving material for cell immobilization, e.g. in 3D bio-printing of cells and has thus, also been employed in the context of this study. To demonstrate the applicability of the established method for functional Ca2+ imaging in gelatin-immobilized suspension cells, a proof-of-concept study was conducted using human peripheral blood model cell lines (Jurkat/T-lymphocytes and THP-1/monocytes), Ca2+ indicators (Fluo-4 and Fura-2) and two different fluorescence microscopy rigs. The data presented that the established methodology is applicable for studying Ca2+ signaling by in vitro high-content functional imaging of [Ca2+]i in suspension cells, including but not restricted to human immune cells.
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Affiliation(s)
- Paul Ritter
- Institute of Medical Biotechnology, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany; Erlangen Graduate School in Advanced Optical Technologies (SAOT), Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Lydia J Bye
- Illawarra Health and Medical Research Institute (IHMRI), University of Wollongong, Wollongong, Australia
| | - Rocio K Finol-Urdaneta
- Illawarra Health and Medical Research Institute (IHMRI), University of Wollongong, Wollongong, Australia
| | - Christian Lesko
- Institute of Medical Biotechnology, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany; Erlangen Graduate School in Advanced Optical Technologies (SAOT), Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - David J Adams
- Illawarra Health and Medical Research Institute (IHMRI), University of Wollongong, Wollongong, Australia
| | - Oliver Friedrich
- Institute of Medical Biotechnology, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany; Erlangen Graduate School in Advanced Optical Technologies (SAOT), Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Daniel F Gilbert
- Institute of Medical Biotechnology, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany; Erlangen Graduate School in Advanced Optical Technologies (SAOT), Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.
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3D Printed Lab-on-a-Chip Platform for Chemical Stimulation and Parallel Analysis of Ion Channel Function. MICROMACHINES 2019; 10:mi10080548. [PMID: 31430884 PMCID: PMC6722671 DOI: 10.3390/mi10080548] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 08/06/2019] [Accepted: 08/16/2019] [Indexed: 12/27/2022]
Abstract
Functional imaging has been a widely established method for the assessment of ion channel function in vitro. Conventional infrastructure used for in vitro functional analysis of ion channels is typically proprietary, non-customizable, expensive, and requires a high level of skill to use and maintain. 3D desktop printing, which is employed in the rapid prototyping field, allows for quick engineering of alternatives to conventional imaging infrastructure that are customizable, low cost, and user friendly. Here, we describe an ultra-low-cost microfluidic lab-on-a-chip (LOC) device manufactured using acrylonitrile butadiene styrene (ABS) for in vitro functional imaging of ion channels that can quickly and easily be reconstructed using three-dimensional (3D) desktop printing. The device is light weight (<5 g), small (20 mm × 49 mm), and extremely low cost (<EUR 1). We simulate fluidics within the printed channels and assess the suitability of the engineered chamber to generate homogeneous mixtures during solution exchange. We demonstrate the usability of the 3D printed microfluidic device in a case study using Fluo-4-loaded human embryonal kidney-derived (HEK293) cells, recombinantly expressing the capsaicin receptor, transient receptor potential vanilloid receptor type 1 (TRPV1), as a model system. In the case study, we confirm its applicability to solution exchange for chemical stimulation and parallel functional time-lapse fluorescence microscopy-based calcium imaging. We assess the suitability of ABS for culturing HEK293 cells inside the microfluidic LOC, based on qualitative analysis of microscopic transmission light images of ABS-exposed HEK293 cells and confirm the previously reported biocompatibility of ABS. To highlight the versatility of the 3D printed microfluidic device, we provide an example for multiplication of the shown concept within a 3D printed multichannel microfluidic LOC to be used, for example, in a higher throughput format for parallelized functional analysis of ion channels. While this work focusses on Ca2+ imaging with TRPV1 channels, the device may also be useful for application with other ion channel types and in vitro models.
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Schmitt MA, Friedrich O, Gilbert DF. Portoporator ©: A portable low-cost electroporation device for gene transfer to cultured cells in biotechnology, biomedical research and education. Biosens Bioelectron 2019; 131:95-103. [PMID: 30826656 DOI: 10.1016/j.bios.2019.02.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 02/03/2019] [Accepted: 02/10/2019] [Indexed: 01/15/2023]
Abstract
Electroporation has been a widely established method for delivering DNA and other material into cells in vitro. Conventional electroporation infrastructure is typically immobile, non-customizable, non-transparent regarding the characteristics of output pulses, and expensive. Here, we describe a portable electroporator for DNA delivery into bacterial cells that can quickly be reconstructed using 3D desktop printing and off-the-shelf components. The device is light weight (700 g), small (70 × 180 × 210 mm) and extremely low-cost (<EUR 130). We provide the electrical circuitry and a detailed parts list for rebuilding the device. We characterize the properties of generated pulses and apply the system for gene delivery into bacterial Dh5α cells. We analyze the transformation efficiency based on the optical density of cell suspensions at 595 nm and on quantitative analysis of images obtained from bacterial cell-grown agar plates using colony forming units as well as confluence as indicators. We demonstrate time-dependency of the transformation efficiency using single pulses of 500 V between 1 and 1000 ms duration and we show that commercially available electroporation cuvettes of 1 mm gap size reveal higher transformation rates compared to cuvettes with 2 mm gap. We benchmark the transformation efficiency obtained using our platform with data from a heat shock-based transformation protocol and with data from a commercially available electroporator and show that our system reveals comparable results as the other techniques in the applied configurations. While this work focuses on genetic manipulation of bacterial cells, the device may also be applicable for delivery of genetic material small molecule or nanomaterials into other cell types, including mammalian cells.
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Affiliation(s)
- Max A Schmitt
- Institute of Medical Biotechnology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Oliver Friedrich
- Institute of Medical Biotechnology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Daniel F Gilbert
- Institute of Medical Biotechnology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.
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7
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Gilbert DF, Mofrad SA, Friedrich O, Wiest J. Proliferation characteristics of cells cultured under periodic versus static conditions. Cytotechnology 2018; 71:443-452. [PMID: 30515656 DOI: 10.1007/s10616-018-0263-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 09/27/2018] [Indexed: 12/13/2022] Open
Abstract
In vitro culture models have become an indispensable tool for assessing a vast variety of biological questions in many scientific fields. However, common in vitro cultures are maintained under static conditions, which do not reflect the in vivo situation and create a non-physiological environment. To assess whether the growth characteristics of cells cultured at pulsed-perfused versus static conditions differ, we observed the growth of differentially cultured cells in vitro by life-cell time-lapse imaging of recombinant HEK293YFPI152L cells, stably expressing yellow fluorescent protein. Cells were grown for ~ 30 h at 37 °C and ambient CO2 concentration in biochips mounted into a custom-designed 3D printed carrier and were imaged at a rate of ten images per hour using a fluorescence microscope with environment control infrastructure. Cells in one chip were maintained under static conditions whereas cells in another chip were recurrently perfused with fresh media. Generated image series were quantitatively analyzed using a custom-modified cell detection software. Imaging data averaged from four biological replicates per culturing condition demonstrate that cells cultured under conventional conditions exhibit an exponential growth rate. In contrast, cells cultured in periodic mode exhibited a non-exponential growth rate. Our data clearly indicate differential growth characteristics of cells cultured under periodic versus static conditions highlighting the impact of the culture conditions on the physiology of cells in vitro.
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Affiliation(s)
- Daniel F Gilbert
- Institute of Medical Biotechnology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany. .,Erlangen Graduate School in Advanced Optical Technologies (SAOT), Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.
| | - Sepideh Abolpour Mofrad
- Institute of Medical Biotechnology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.,Erlangen Graduate School in Advanced Optical Technologies (SAOT), Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Oliver Friedrich
- Institute of Medical Biotechnology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.,Erlangen Graduate School in Advanced Optical Technologies (SAOT), Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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8
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Systematic RNA-interference in primary human monocyte-derived macrophages: A high-throughput platform to study foam cell formation. Sci Rep 2018; 8:10516. [PMID: 30002403 PMCID: PMC6043567 DOI: 10.1038/s41598-018-28790-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 06/29/2018] [Indexed: 12/21/2022] Open
Abstract
Macrophage-derived foam cells are key regulators of atherogenesis. They accumulate in atherosclerotic plaques and support inflammatory processes by producing cytokines and chemokines. Identifying factors that regulate macrophage lipid uptake may reveal therapeutic targets for coronary artery disease (CAD). Here, we establish a high-throughput screening workflow to systematically identify genes that impact the uptake of DiI-labeled low-density lipoprotein (LDL) into monocyte-derived primary human macrophages. For this, monocytes isolated from peripheral blood were seeded onto 384-well plates, solid-phase transfected with siRNAs, differentiated in vitro into macrophages, and LDL-uptake per cell was measured by automated microscopy and quantitative image analysis. We applied this workflow to study how silencing of 89 genes impacts LDL-uptake into cells from 16 patients with CAD and 16 age-matched controls. Silencing of four novel genes (APOC1, CMTM6, FABP4, WBP5) reduced macrophage LDL-uptake. Additionally, knockdown of the chemokine receptor CXCR4 reduced LDL-uptake, most likely through a G-protein coupled mechanism that involves the CXCR4 ligand macrophage-induced factor (MIF), but is independent of CXCL12. We introduce a high-throughput strategy to systematically study gene function directly in primary CAD-patient cells. Our results propose a function for the MIF/CXCR4 signaling pathway, as well as several novel candidate genes impacting lipid uptake into human macrophages.
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9
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Scharin-Mehlmann M, Häring A, Rommel M, Dirnecker T, Friedrich O, Frey L, Gilbert DF. Nano- and Micro-Patterned S-, H-, and X-PDMS for Cell-Based Applications: Comparison of Wettability, Roughness, and Cell-Derived Parameters. Front Bioeng Biotechnol 2018; 6:51. [PMID: 29765941 PMCID: PMC5938557 DOI: 10.3389/fbioe.2018.00051] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 04/16/2018] [Indexed: 12/12/2022] Open
Abstract
Polydimethylsiloxane (PDMS) is a promising biomaterial for generating artificial extracellular matrix (ECM) like patterned topographies, yet its hydrophobic nature limits its applicability to cell-based approaches. Although plasma treatment can enhance the wettability of PDMS, the surface is known to recover its hydrophobicity within a few hours after exposure to air. To investigate the capability of a novel PDMS-type (X-PDMS) for in vitro based assessment of physiological cell properties, we designed and fabricated plane as well as nano- and micrometer-scaled pillar-patterned growth substrates using the elastomer types S-, H- and X-PDMS, which were fabricated from commercially available components. Most importantly, we compared X-PDMS based growth substrates which have not yet been investigated in this context with H- as well as well-known S-PDMS based substrates. Due to its applicability to fabricating nanometer-sized topographic features with high accuracy and pattern fidelity, this material may be of high relevance for specific biomedical applications. To assess their applicability to cell-based approaches, we characterized the generated surfaces using water contact angle (WCA) measurement and atomic force microscopy (AFM) as indicators of wettability and roughness, respectively. We further assessed cell number, cell area and cellular elongation as indirect measures of cellular viability and adhesion by image cytometry and phenotypic profiling, respectively, using Calcein and Hoechst 33342 stained human foreskin fibroblasts as a model system. We show for the first time that different PDMS types are differently sensitive to plasma treatment. We further demonstrate that surface hydrophobicity changes along with changing height of the pillar-structures. Our data indicate that plane and structured X-PDMS shows cytocompatibility and adhesive properties comparable to the previously described elastomer types S- and H-PDMS. We conclude that nanometer-sized structuring of X-PDMS may serve as a powerful method for altering surface properties toward production of biomedical devices for cell-based applications.
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Affiliation(s)
- Marina Scharin-Mehlmann
- Chair of Electron Devices, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Aaron Häring
- Chair of Electron Devices, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.,Institute of Medical Biotechnology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Mathias Rommel
- Fraunhofer Institute for Integrated Systems and Device Technology (IISB), Erlangen, Germany
| | - Tobias Dirnecker
- Chair of Electron Devices, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Oliver Friedrich
- Institute of Medical Biotechnology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.,Erlangen Graduate School in Advanced Optical Technologies (SAOT), Erlangen, Germany
| | - Lothar Frey
- Chair of Electron Devices, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.,Fraunhofer Institute for Integrated Systems and Device Technology (IISB), Erlangen, Germany.,Erlangen Graduate School in Advanced Optical Technologies (SAOT), Erlangen, Germany
| | - Daniel F Gilbert
- Institute of Medical Biotechnology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.,Erlangen Graduate School in Advanced Optical Technologies (SAOT), Erlangen, Germany
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Roeper M, Braun-Dullaeus RC, Weinert S. Semiautomatic High-Content Analysis of Complex Images from Cocultures of Vascular Smooth Muscle Cells and Macrophages: A CellProfiler Showcase. SLAS DISCOVERY 2017; 22:837-847. [PMID: 28346101 DOI: 10.1177/2472555217691451] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Automatization in microscopy, cell culture, and the ease of digital imagery allow obtainment of more information from single samples and upscaling of image-based analysis to high-content approaches. Simple segmentation algorithms of biological imagery are nowadays widely spread in biomedical research, but processing of complex sample structures, for example, variable sample compositions, cell shapes, and sizes, and rare events remains a difficult task. As there is no perfect method for image segmentation and fully automatic image analysis of complex content, we aimed to succeed by identification of unique and reliable features within the sample. Through exemplary use of a coculture of vascular smooth muscle cells (VSMCs) and macrophages (MPs), we demonstrate how rare interactions within this highly variable sample type can be analyzed. Because of limitations in immunocytochemistry in our specific setup, we developed a semiautomatic approach to examine the interaction of lipid-laden MPs with VSMCs under hypoxic conditions based on nuclei morphology by high-content analysis using the open-source software CellProfiler ( www.cellprofiler.org ). We provide evidence that, in comparison with fully automatic analysis, a low threshold within the analysis workflow and subsequent manual control save time, while providing more objective and reliable results.
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Affiliation(s)
- Matthias Roeper
- 1 Internal Medicine, Department of Cardiology and Angiology, Health Campus Immunology, Infectiology and Inflammation, Magdeburg University, Magdeburg, Saxony-Anhalt, Germany
| | - Ruediger C Braun-Dullaeus
- 1 Internal Medicine, Department of Cardiology and Angiology, Health Campus Immunology, Infectiology and Inflammation, Magdeburg University, Magdeburg, Saxony-Anhalt, Germany
| | - Sönke Weinert
- 1 Internal Medicine, Department of Cardiology and Angiology, Health Campus Immunology, Infectiology and Inflammation, Magdeburg University, Magdeburg, Saxony-Anhalt, Germany
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11
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Dakhil H, Wierschem A. Average Rheological Quantities of Cells in Monolayers. Methods Mol Biol 2017; 1601:257-266. [PMID: 28470532 DOI: 10.1007/978-1-4939-6960-9_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Measuring rheological properties of cells in monolayers enables quantifying average cell properties in single experimental runs despite large cell-to-cell variations. Here, we describe how to modify a commercial rotational rheometer to accomplish the necessary precision for a monolayer rheometer and we delineate the steps for setting up experiments detecting average viscoelastic cell properties.
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Affiliation(s)
- Haider Dakhil
- Institute of Fluid Mechanics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Cauerstr. 4, Erlangen, 91058, Germany
- Faculty of Engineering, University of Kufa, Kufa, 21, 00964, Najaf, Iraq
| | - Andreas Wierschem
- Institute of Fluid Mechanics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Cauerstr. 4, Erlangen, 91058, Germany.
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12
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Lynch JW, Zhang Y, Talwar S, Estrada-Mondragon A. Glycine Receptor Drug Discovery. ADVANCES IN PHARMACOLOGY 2017; 79:225-253. [DOI: 10.1016/bs.apha.2017.01.003] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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13
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Islam R, Keramidas A, Xu L, Durisic N, Sah P, Lynch JW. Ivermectin-Activated, Cation-Permeable Glycine Receptors for the Chemogenetic Control of Neuronal Excitation. ACS Chem Neurosci 2016; 7:1647-1657. [PMID: 27611437 DOI: 10.1021/acschemneuro.6b00168] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The ability to control neuronal activation is rapidly advancing our understanding of brain function and is widely viewed as having eventual therapeutic application. Although several highly effective optogenetic, optochemical genetic, and chemogenetic techniques have been developed for this purpose, new approaches may provide better solutions for addressing particular questions and would increase the number of neuronal populations that can be controlled independently. An early chemogenetic neuronal silencing method employed a glutamate receptor Cl- channel engineered for activation by 1-3 nM ivermectin. This construct has been validated in vivo. Here, we sought to develop cation-permeable ivermectin-gated receptors that were either maximally Ca2+-permeable so as to induce neuro-excitotoxic cell death or minimally Ca2+-permeable so as to depolarize neurons with minimal excitotoxic risk. Our constructs were based on the human α1 glycine receptor Cl- channel due to its high conductance, human origin, high ivermectin sensitivity (once mutated), and because pore mutations that render it permeable to Na+ alone or Na+ plus Ca2+ are well characterized. We developed a Ca2+-impermeable excitatory receptor by introducing the F207A/P-2'Δ/A-1'E/T13'V/A288G mutations and a Ca2+-permeable excitatory receptor by introducing the F207A/A-1'E/A288G mutations. The latter receptor efficiently induces cell death and strongly depolarizes neurons at nanomolar ivermectin concentrations.
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Affiliation(s)
- Robiul Islam
- Queensland
Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Angelo Keramidas
- Queensland
Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Li Xu
- Queensland
Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Nela Durisic
- Queensland
Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Pankaj Sah
- Queensland
Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Joseph W. Lynch
- Queensland
Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
- School
of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
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14
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Step-by-step guide to building an inexpensive 3D printed motorized positioning stage for automated high-content screening microscopy. Biosens Bioelectron 2016; 92:472-481. [PMID: 27840039 DOI: 10.1016/j.bios.2016.10.078] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 10/21/2016] [Accepted: 10/25/2016] [Indexed: 01/16/2023]
Abstract
High-content screening microscopy relies on automation infrastructure that is typically proprietary, non-customizable, costly and requires a high level of skill to use and maintain. The increasing availability of rapid prototyping technology makes it possible to quickly engineer alternatives to conventional automation infrastructure that are low-cost and user-friendly. Here, we describe a 3D printed inexpensive open source and scalable motorized positioning stage for automated high-content screening microscopy and provide detailed step-by-step instructions to re-building the device, including a comprehensive parts list, 3D design files in STEP (Standard for the Exchange of Product model data) and STL (Standard Tessellation Language) format, electronic circuits and wiring diagrams as well as software code. System assembly including 3D printing requires approx. 30h. The fully assembled device is light-weight (1.1kg), small (33×20×8cm) and extremely low-cost (approx. EUR 250). We describe positioning characteristics of the stage, including spatial resolution, accuracy and repeatability, compare imaging data generated with our device to data obtained using a commercially available microplate reader, demonstrate its suitability to high-content microscopy in 96-well high-throughput screening format and validate its applicability to automated functional Cl-- and Ca2+-imaging with recombinant HEK293 cells as a model system. A time-lapse video of the stage during operation and as part of a custom assembled screening robot can be found at https://vimeo.com/158813199.
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15
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Gilbert DF, Stebbing MJ, Kuenzel K, Murphy RM, Zacharewicz E, Buttgereit A, Stokes L, Adams DJ, Friedrich O. Store-Operated Ca 2+ Entry (SOCE) and Purinergic Receptor-Mediated Ca 2+ Homeostasis in Murine bv2 Microglia Cells: Early Cellular Responses to ATP-Mediated Microglia Activation. Front Mol Neurosci 2016; 9:111. [PMID: 27840602 PMCID: PMC5083710 DOI: 10.3389/fnmol.2016.00111] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 10/14/2016] [Indexed: 12/31/2022] Open
Abstract
Microglia activation is a neuroinflammatory response to parenchymal damage with release of intracellular metabolites, e.g., purines, and signaling molecules from damaged cells. Extracellular purines can elicit Ca2+-mediated microglia activation involving P2X/P2Y receptors with metabotropic (P2Y) and ionotropic (P2X) cell signaling in target cells. Such microglia activation results in increased phagocytic activity, activation of their inflammasome and release of cytokines to sustain neuroinflammatory (so-called M1/M2 polarization). ATP-induced activation of ionotropic P2X4 and P2X7 receptors differentially induces receptor-operated Ca2+ entry (ROCE). Although store-operated Ca2+ entry (SOCE) was identified to modulate ROCE in primary microglia, its existence and role in one of the most common murine microglia cell line, BV2, is unknown. To dissect SOCE from ROCE in BV2 cells, we applied high-resolution multiphoton Ca2+ imaging. After depleting internal Ca2+ stores, SOCE was clearly detectable. High ATP concentrations (1 mM) elicited sustained increases in intracellular [Ca2+]i whereas lower concentrations (≤100 μM) also induced Ca2+ oscillations. These differential responses were assigned to P2X7 and P2X4 activation, respectively. Pharmacologically inhibiting P2Y and P2X responses did not affect SOCE, and in fact, P2Y-responses were barely detectable in BV2 cells. STIM1S content was significantly upregulated by 1 mM ATP. As P2X-mediated Ca2+ oscillations were rare events in single cells, we implemented a high-content screening approach that allows to record Ca2+ signal patterns from a large number of individual cells at lower optical resolution. Using automated classifier analysis, several drugs (minocycline, U73122, U73343, wortmannin, LY294002, AZ10606120) were tested on their profile to act on Ca2+ oscillations (P2X4) and sustained [Ca2+]i increases. We demonstrate specific drug effects on purinergic Ca2+ pathways and provide new pharmacological insights into Ca2+ oscillations in BV2 cells. For example, minocycline inhibits both P2X7- and P2X4-mediated Ca2+-responses, and this may explain its anti-inflammatory action in neuroinflammatory disease. As a technical result, our novel automated bio-screening approach provides a biomedical engineering platform to allow high-content drug library screens to study neuro-inflammation in vitro.
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Affiliation(s)
- Daniel F Gilbert
- Department of Chemical and Biological Engineering, Institute of Medical Biotechnology, Friedrich-Alexander-Universität Erlangen-NürnbergErlangen, Germany; Erlangen Graduate School in Advanced Optical Technologies, Friedrich-Alexander-Universität Erlangen-NürnbergErlangen, Germany
| | - Martin J Stebbing
- Health Innovations Research Institute, Royal Melbourne Institute of Technology University, Melbourne VIC, Australia
| | - Katharina Kuenzel
- Department of Chemical and Biological Engineering, Institute of Medical Biotechnology, Friedrich-Alexander-Universität Erlangen-NürnbergErlangen, Germany; Erlangen Graduate School in Advanced Optical Technologies, Friedrich-Alexander-Universität Erlangen-NürnbergErlangen, Germany
| | - Robyn M Murphy
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne VIC, Australia
| | - Evelyn Zacharewicz
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne VIC, Australia
| | - Andreas Buttgereit
- Department of Chemical and Biological Engineering, Institute of Medical Biotechnology, Friedrich-Alexander-Universität Erlangen-Nürnberg Erlangen, Germany
| | - Leanne Stokes
- Health Innovations Research Institute, Royal Melbourne Institute of Technology University, Melbourne VIC, Australia
| | - David J Adams
- Health Innovations Research Institute, Royal Melbourne Institute of Technology University, Melbourne VIC, Australia
| | - Oliver Friedrich
- Department of Chemical and Biological Engineering, Institute of Medical Biotechnology, Friedrich-Alexander-Universität Erlangen-NürnbergErlangen, Germany; Erlangen Graduate School in Advanced Optical Technologies, Friedrich-Alexander-Universität Erlangen-NürnbergErlangen, Germany; Health Innovations Research Institute, Royal Melbourne Institute of Technology University, MelbourneVIC, Australia
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Spitzer P, Condic M, Herrmann M, Oberstein TJ, Scharin-Mehlmann M, Gilbert DF, Friedrich O, Grömer T, Kornhuber J, Lang R, Maler JM. Amyloidogenic amyloid-β-peptide variants induce microbial agglutination and exert antimicrobial activity. Sci Rep 2016; 6:32228. [PMID: 27624303 PMCID: PMC5021948 DOI: 10.1038/srep32228] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 08/04/2016] [Indexed: 11/09/2022] Open
Abstract
Amyloid-β (Aβ) peptides are the main components of the plaques found in the brains of patients with Alzheimer's disease. However, Aβ peptides are also detectable in secretory compartments and peripheral blood contains a complex mixture of more than 40 different modified and/or N- and C-terminally truncated Aβ peptides. Recently, anti-infective properties of Aβ peptides have been reported. Here, we investigated the interaction of Aβ peptides of different lengths with various bacterial strains and the yeast Candida albicans. The amyloidogenic peptides Aβ1-42, Aβ2-42, and Aβ3p-42 but not the non-amyloidogenic peptides Aβ1-40 and Aβ2-40 bound to microbial surfaces. As observed by immunocytochemistry, scanning electron microscopy and Gram staining, treatment of several bacterial strains and Candida albicans with Aβ peptide variants ending at position 42 (Aβx-42) caused the formation of large agglutinates. These aggregates were not detected after incubation with Aβx-40. Furthermore, Aβx-42 exerted an antimicrobial activity on all tested pathogens, killing up to 80% of microorganisms within 6 h. Aβ1-40 only had a moderate antimicrobial activity against C. albicans. Agglutination of Aβ1-42 was accelerated in the presence of microorganisms. These data demonstrate that the amyloidogenic Aβx-42 variants have antimicrobial activity and may therefore act as antimicrobial peptides in the immune system.
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Affiliation(s)
- Philipp Spitzer
- Department of Psychiatry and Psychotherapy, Friedrich-Alexander-University Erlangen-Nuremberg, Schwabachanlage 6, D-91054 Erlangen, Germany
| | - Mateja Condic
- Department of Psychiatry and Psychotherapy, Friedrich-Alexander-University Erlangen-Nuremberg, Schwabachanlage 6, D-91054 Erlangen, Germany
| | - Martin Herrmann
- Department of Medicine III, Institute for Clinical Immunology, Friedrich-Alexander-University Erlangen-Nuremberg, Gluecksstraße 4a, D-91054 Erlangen, Germany
| | - Timo Jan Oberstein
- Department of Psychiatry and Psychotherapy, Friedrich-Alexander-University Erlangen-Nuremberg, Schwabachanlage 6, D-91054 Erlangen, Germany
| | - Marina Scharin-Mehlmann
- Electron Devices, Friedrich-Alexander-University Erlangen-Nuremberg, Cauerstraße 6, D-91058 Erlangen, Germany
| | - Daniel F Gilbert
- Institute of Medical Biotechnology, Friedrich-Alexander-University Erlangen-Nuremberg, Paul-Gordan-Str. 3, D-91052 Erlangen, Germany
| | - Oliver Friedrich
- Institute of Medical Biotechnology, Friedrich-Alexander-University Erlangen-Nuremberg, Paul-Gordan-Str. 3, D-91052 Erlangen, Germany
| | - Teja Grömer
- Department of Psychiatry and Psychotherapy, Friedrich-Alexander-University Erlangen-Nuremberg, Schwabachanlage 6, D-91054 Erlangen, Germany
| | - Johannes Kornhuber
- Department of Psychiatry and Psychotherapy, Friedrich-Alexander-University Erlangen-Nuremberg, Schwabachanlage 6, D-91054 Erlangen, Germany
| | - Roland Lang
- Institute of Clinical Microbiology, Immunology and Hygiene, Friedrich-Alexander-University Erlangen-Nuremberg, Wasserturmstr. 3/5, D-91054 Erlangen, Germany
| | - Juan Manuel Maler
- Department of Psychiatry and Psychotherapy, Friedrich-Alexander-University Erlangen-Nuremberg, Schwabachanlage 6, D-91054 Erlangen, Germany
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Kuenzel K, Friedrich O, Gilbert DF. A Recombinant Human Pluripotent Stem Cell Line Stably Expressing Halide-Sensitive YFP-I152L for GABAAR and GlyR-Targeted High-Throughput Drug Screening and Toxicity Testing. Front Mol Neurosci 2016; 9:51. [PMID: 27445687 PMCID: PMC4923258 DOI: 10.3389/fnmol.2016.00051] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 06/13/2016] [Indexed: 01/29/2023] Open
Abstract
GABAARs and GlyRs are considered attractive drug targets for therapeutic intervention and are also increasingly recognized in the context of in vitro neurotoxicity (NT) and developmental neurotoxicity (DNT) testing. However, systematic human-specific GABAAR and GlyR-targeted drug screening and toxicity testing is hampered due to lack of appropriate in vitro models that express native GABAARs and GlyRs. We have established a human pluripotent stem cell line (NT2) stably expressing YFP-I152L, a halide-sensitive variant of yellow fluorescent protein (YFP), allowing for fluorescence-based functional analysis of chloride channels. Upon stimulation with retinoic acid, NT2 cells undergo neuronal differentiation and allow pharmacological and toxicological evaluation of native GABAARs and GlyRs at different stages of brain maturation. We applied the cell line in concentration-response experiments with the neurotransmitters GABA and glycine as well as with the drugs strychnine, picrotoxin, fipronil, lindane, bicuculline, and zinc and demonstrate that the established in vitro model is applicable to GABAAR and GlyR-targeted pharmacological and toxicological profiling. We quantified the proportion of GABAAR and GlyR-sensitive cells, respectively, and identified percentages of approximately 20% each within the overall populations, rendering the cells a suitable model for systematic in vitro GABAAR and GlyR-targeted screening in the context of drug development and NT/DNT testing.
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Affiliation(s)
- Katharina Kuenzel
- Department of Chemical and Biological Engineering, Institute of Medical Biotechnology, Friedrich-Alexander-Universität Erlangen-NürnbergErlangen, Germany; Erlangen Graduate School in Advanced Optical Technologies, Friedrich-Alexander-Universität Erlangen-NürnbergErlangen, Germany
| | - Oliver Friedrich
- Department of Chemical and Biological Engineering, Institute of Medical Biotechnology, Friedrich-Alexander-Universität Erlangen-NürnbergErlangen, Germany; Erlangen Graduate School in Advanced Optical Technologies, Friedrich-Alexander-Universität Erlangen-NürnbergErlangen, Germany
| | - Daniel F Gilbert
- Department of Chemical and Biological Engineering, Institute of Medical Biotechnology, Friedrich-Alexander-Universität Erlangen-NürnbergErlangen, Germany; Erlangen Graduate School in Advanced Optical Technologies, Friedrich-Alexander-Universität Erlangen-NürnbergErlangen, Germany
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18
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A portable low-cost long-term live-cell imaging platform for biomedical research and education. Biosens Bioelectron 2015; 64:639-49. [DOI: 10.1016/j.bios.2014.09.061] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 09/18/2014] [Accepted: 09/22/2014] [Indexed: 11/22/2022]
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19
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Zhang X, Boutros M. A novel phenotypic dissimilarity method for image-based high-throughput screens. BMC Bioinformatics 2013; 14:336. [PMID: 24256072 PMCID: PMC4225524 DOI: 10.1186/1471-2105-14-336] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Accepted: 11/13/2013] [Indexed: 02/02/2023] Open
Abstract
Background Discovering functional relationships of genes through cell-based phenotyping has become an important approach in functional genomics. High-throughput imaging offers the ability to quantitatively assess complex phenotypes after perturbation by RNA interference (RNAi). Such image-based high-throughput RNAi screening studies have facilitated the discovery of novel components of gene networks and their interactions. Images generated by automated microscopy are typically analyzed by extracting quantitative features of individual cells, resulting in large multidimensional data sets. Robust and sensitive methods to interpret these data sets and to derive biologically relevant information in a high-throughput and unbiased manner remain to be developed. Results Here we propose a new analysis method, PhenoDissim, which computes the phenotypic dissimilarity between cell populations via Support Vector Machine classification and cross validation. Applying this method to a kinome RNAi screening data set, we demonstrate that the proposed method shows a good replicate reproducibility, separation of controls and clustering quality, and we are able to identify siRNA phenotypes and discover potential functional links between genes. Conclusions PhenoDissim is a novel analysis method for image-based high-throughput screen, relying on two parameters which can be automatically optimized without a priori knowledge. PhenoDissim is freely available as an R package.
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Affiliation(s)
- Xian Zhang
- German Cancer Research Center (DKFZ), Div, Signaling and Functional Genomics and Department of Cell and Molecular Biology, Medical Faculty Mannheim, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany.
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20
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Balansa W, Islam R, Gilbert DF, Fontaine F, Xiao X, Zhang H, Piggott AM, Lynch JW, Capon RJ. Australian marine sponge alkaloids as a new class of glycine-gated chloride channel receptor modulator. Bioorg Med Chem 2013; 21:4420-5. [PMID: 23685178 DOI: 10.1016/j.bmc.2013.04.061] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 04/10/2013] [Accepted: 04/18/2013] [Indexed: 11/30/2022]
Abstract
Chemical analysis of a specimen of the sponge Ianthella cf. flabelliformis returned two new sesquiterpene glycinyl lactams, ianthellalactams A (1) and B (2), the known sponge sesquiterpene dictyodendrillin (3) and its ethanolysis artifact ethyl dictyodendrillin (4), and five known sponge indole alkaloids, aplysinopsin (5), 8E-3'-deimino-3'-oxoaplysinopsin (6), 8Z-3'-deimino-3'-oxoaplysinopsin (7), dihydroaplysinopsin (8) and tubastrindole B (9). The equilibrated mixture 6/7 exhibited glycine-gated chloride channel receptor (GlyR) antagonist activity with a bias towards α3 over α1 GlyR, while tubastrindole B (9) exhibited a bias towards α1 over α3 GlyR. At low- to sub-micromolar concentrations, 9 was also a selective potentiator of α1 GlyR, with no effect on α3 GlyR-a pharmacology that could prove useful in the treatment of movement disorders such as spasticity and hyperekplexia. Our investigations into the GlyR modulatory properties of 1-9 were further supported by the synthesis of a number of structurally related indole alkaloids.
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Affiliation(s)
- Walter Balansa
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia
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21
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Talwar S, Lynch JW, Gilbert DF. Fluorescence-based high-throughput functional profiling of ligand-gated ion channels at the level of single cells. PLoS One 2013; 8:e58479. [PMID: 23520514 PMCID: PMC3592791 DOI: 10.1371/journal.pone.0058479] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Accepted: 02/06/2013] [Indexed: 12/26/2022] Open
Abstract
Ion channels are involved in many physiological processes and are attractive targets for therapeutic intervention. Their functional properties vary according to their subunit composition, which in turn varies in a developmental and tissue-specific manner and as a consequence of pathophysiological events. Understanding this diversity requires functional analysis of ion channel properties in large numbers of individual cells. Functional characterisation of ligand-gated channels involves quantitating agonist and drug dose-response relationships using electrophysiological or fluorescence-based techniques. Electrophysiology is limited by low throughput and high-throughput fluorescence-based functional evaluation generally does not enable the characterization of the functional properties of each individual cell. Here we describe a fluorescence-based assay that characterizes functional channel properties at single cell resolution in high throughput mode. It is based on progressive receptor activation and iterative fluorescence imaging and delivers >100 dose-responses in a single well of a 384-well plate, using α1-3 homomeric and αβ heteromeric glycine receptor (GlyR) chloride channels as a model system. We applied this assay with transiently transfected HEK293 cells co-expressing halide-sensitive yellow fluorescent protein and different GlyR subunit combinations. Glycine EC50 values of different GlyR isoforms were highly correlated with published electrophysiological data and confirm previously reported pharmacological profiles for the GlyR inhibitors, picrotoxin, strychnine and lindane. We show that inter and intra well variability is low and that clustering of functional phenotypes permits identification of drugs with subunit-specific pharmacological profiles. As this method dramatically improves the efficiency with which ion channel populations can be characterized in the context of cellular heterogeneity, it should facilitate systems-level analysis of ion channel properties in health and disease and the discovery of therapeutics to reverse pathological alterations.
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Affiliation(s)
- Sahil Talwar
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Joseph W. Lynch
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
- School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Daniel F. Gilbert
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
- Institute of Medical Biotechnology, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
- * E-mail:
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22
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Balansa W, Islam R, Fontaine F, Piggott AM, Zhang H, Xiao X, Webb TI, Gilbert DF, Lynch JW, Capon RJ. Sesterterpene glycinyl-lactams: a new class of glycine receptor modulator from Australian marine sponges of the genus Psammocinia. Org Biomol Chem 2013; 11:4695-701. [DOI: 10.1039/c3ob40861b] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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23
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Serva A, Knapp B, Tsai YT, Claas C, Lisauskas T, Matula P, Harder N, Kaderali L, Rohr K, Erfle H, Eils R, Braga V, Starkuviene V. miR-17-5p regulates endocytic trafficking through targeting TBC1D2/Armus. PLoS One 2012; 7:e52555. [PMID: 23285084 PMCID: PMC3527550 DOI: 10.1371/journal.pone.0052555] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Accepted: 11/15/2012] [Indexed: 01/07/2023] Open
Abstract
miRNA cluster miR-17-92 is known as oncomir-1 due to its potent oncogenic function. miR-17-92 is a polycistronic cluster that encodes 6 miRNAs, and can both facilitate and inhibit cell proliferation. Known targets of miRNAs encoded by this cluster are largely regulators of cell cycle progression and apoptosis. Here, we show that miRNAs encoded by this cluster and sharing the seed sequence of miR-17 exert their influence on one of the most essential cellular processes – endocytic trafficking. By mRNA expression analysis we identified that regulation of endocytic trafficking by miR-17 can potentially be achieved by targeting of a number of trafficking regulators. We have thoroughly validated TBC1D2/Armus, a GAP of Rab7 GTPase, as a novel target of miR-17. Our study reveals regulation of endocytic trafficking as a novel function of miR-17, which might act cooperatively with other functions of miR-17 and related miRNAs in health and disease.
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Affiliation(s)
- Andrius Serva
- BioQuant, University of Heidelberg, Heidelberg, Germany
| | - Bettina Knapp
- BioQuant, University of Heidelberg, Heidelberg, Germany
- Institute for Medical Informatics and Biometry, University of Technology Dresden, Dresden, Germany
| | - Yueh-Tso Tsai
- BioQuant, University of Heidelberg, Heidelberg, Germany
| | | | | | - Petr Matula
- Integrative Bioinformatics and Systems Biology, DKFZ, BioQuant and Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, Heidelberg, Germany
- Center for Biomedical Image Analysis, Faculty of Informatics, Masaryk University, Brno, Czech Republic
| | - Nathalie Harder
- Integrative Bioinformatics and Systems Biology, DKFZ, BioQuant and Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, Heidelberg, Germany
| | - Lars Kaderali
- BioQuant, University of Heidelberg, Heidelberg, Germany
- Institute for Medical Informatics and Biometry, University of Technology Dresden, Dresden, Germany
| | - Karl Rohr
- Integrative Bioinformatics and Systems Biology, DKFZ, BioQuant and Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, Heidelberg, Germany
| | - Holger Erfle
- BioQuant, University of Heidelberg, Heidelberg, Germany
| | - Roland Eils
- Integrative Bioinformatics and Systems Biology, DKFZ, BioQuant and Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, Heidelberg, Germany
| | - Vania Braga
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
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Abstract
The discovery of RNA interference (RNAi) and the development of technologies exploiting its biology have enabled scientists to rapidly examine the consequences of depleting a particular gene product in a cell or an animal. The availability of genome-wide RNAi libraries targeting the mouse and human genomes has made it possible to carry out large scale, phenotype-based screens, which have yielded seminal information on diverse cellular processes ranging from virology to cancer biology. Today, several strategies are available to perform RNAi screens, each with their own technical and monetary considerations. Special care and budgeting must be taken into account during the design of these screens in order to obtain reliable results. In this review, we discuss a number of critical aspects to consider when planning an effective RNAi screening strategy, including selecting the right biological system, designing an appropriate selection scheme, optimizing technical aspects of the screen, and validating and verifying the hits. Similar to an artistic production, what happens behind the screen has a direct impact on its success.
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Affiliation(s)
- Eric Campeau
- Translational Biology Group, Calgary, AB, Canada.
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25
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Tängemo C, Weber D, Theiss S, Mengel E, Runz H. Niemann-Pick Type C disease: characterizing lipid levels in patients with variant lysosomal cholesterol storage. J Lipid Res 2011; 52:813-25. [PMID: 21245028 DOI: 10.1194/jlr.p013524] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A central feature of Niemann-Pick Type C (NPC) disease is sequestration of cholesterol and glycosphingolipids in lysosomes. A large phenotypic variability, on both a clinical as well as a molecular level, challenges NPC diagnosis. For example, substantial difficulties in identifying or excluding NPC in a patient exist in cases with a "variant" biochemical phenotype, where cholesterol levels in cultured fibroblasts, the primary diagnostic indicator, are only moderately elevated. Here we apply quantitative microscopy as an accurate and objective diagnostic tool to measure cholesterol accumulation at the level of single cells. When employed to characterize cholesterol enrichment in fibroblasts from 20 NPC patients and 11 controls, considerable heterogeneity became evident both within the population of cells cultured from one individual as well as between samples from different probands. An obvious correlation between biochemical phenotype and clinical disease course was not apparent from our dataset. However, plasma levels of HDL-cholesterol (HDL-c) tended to be in the normal range in patients with a "variant" as opposed to a "classic" biochemical phenotype. Attenuated lysosomal cholesterol accumulation in "variant" cells was associated with detectable NPC1 protein and residual capability to upregulate expression of ABCA1 in response to LDL. Taken together, our approach opens perspectives not only to support diagnosis, but also to better characterize mechanisms impacting cholesterol accumulation in NPC patient-derived cells.
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Affiliation(s)
- Carolina Tängemo
- Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany
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Gebhardt FM, Mitrovic AD, Gilbert DF, Vandenberg RJ, Lynch JW, Dodd PR. Exon-skipping splice variants of excitatory amino acid transporter-2 (EAAT2) form heteromeric complexes with full-length EAAT2. J Biol Chem 2010; 285:31313-24. [PMID: 20688910 PMCID: PMC2951206 DOI: 10.1074/jbc.m110.153494] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2010] [Revised: 08/02/2010] [Indexed: 12/12/2022] Open
Abstract
The glial transporter excitatory amino acid transporter-2 (EAAT2) is the main mediator of glutamate clearance in brain. The wild-type transporter (EAAT2wt) forms trimeric membrane complexes in which each protomer functions autonomously. Several EAAT2 variants are found in control and Alzheimer-diseased human brains; their expression increases with pathological severity. These variants might alter EAAT2wt-mediated transport by abrogating membrane trafficking, or by changing the configuration or functionality of the assembled transporter complex. HEK293 cells were transfected with EAAT2wt; EAAT2b, a C-terminal variant; or either of two exon-skipping variants: alone or in combination. Surface biotinylation studies showed that only the exon-7 deletion variant was not trafficked to the membrane when transfected alone, and that all variants could reach the membrane when co-transfected with EAAT2wt. Fluorescence resonance energy transfer (FRET) studies showed that co-transfected EAAT2wt and EAAT2 splice variants were expressed in close proximity. Glutamate transporter function was measured using a whole cell patch clamp technique, or by changes in membrane potential indexed by a voltage-sensitive fluorescent dye (FMP assay): the two methods gave comparable results. Cells transfected with EAAT2wt or EAAT2b showed glutamate-dependent membrane potential changes consistent with functional expression. Cells transfected with EAAT2 exon-skipping variants alone gave no response to glutamate. Co-transfection of EAAT2wt (or EAAT2b) and splice variants in various ratios significantly raised glutamate EC(50) and decreased Hill coefficients. We conclude that exon-skipping variants form heteromeric complexes with EAAT2wt or EAAT2b that traffic to the membrane but show reduced glutamate-dependent activity. This could allow glutamate to accumulate extracellularly and promote excitotoxicity.
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Affiliation(s)
| | - Ann D. Mitrovic
- the Discipline of Pharmacology and Bosch Institute, University of Sydney, Sydney 2006, Australia
| | - Daniel F. Gilbert
- the Queensland Brain Institute and School of Biomedical Sciences, University of Queensland, Brisbane 4072 and
| | - Robert J. Vandenberg
- the Discipline of Pharmacology and Bosch Institute, University of Sydney, Sydney 2006, Australia
| | - Joseph W. Lynch
- the Queensland Brain Institute and School of Biomedical Sciences, University of Queensland, Brisbane 4072 and
| | - Peter R. Dodd
- From the School of Chemistry and Molecular Biosciences and
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Falschlehner C, Steinbrink S, Erdmann G, Boutros M. High-throughput RNAi screening to dissect cellular pathways: A how-to guide. Biotechnol J 2010; 5:368-76. [DOI: 10.1002/biot.200900277] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Gilbert DF, Islam R, Lynagh T, Lynch JW, Webb TI. High Throughput Techniques for Discovering New Glycine Receptor Modulators and their Binding Sites. Front Mol Neurosci 2009; 2:17. [PMID: 19949449 PMCID: PMC2782790 DOI: 10.3389/neuro.02.017.2009] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2009] [Accepted: 09/27/2009] [Indexed: 11/13/2022] Open
Abstract
The inhibitory glycine receptor (GlyR) is a member of the Cys-loop receptor family that mediates inhibitory neurotransmission in the central nervous system. These receptors are emerging as potential drug targets for inflammatory pain, immunomodulation, spasticity and epilepsy. Antagonists that specifically inhibit particular GlyR isoforms are also required as pharmacological probes for elucidating the roles of particular GlyR isoforms in health and disease. Although a substantial number of both positive and negative GlyR modulators have been identified, very few of these are specific for the GlyR over other receptor types. Thus, the potential of known compounds as either therapeutic leads or pharmacological probes is limited. It is therefore surprising that there have been few published studies describing attempts to discover novel GlyR isoform-specific modulators. The first aim of this review is to consider various methods for efficiently screening compounds against these receptors. We conclude that an anion sensitive yellow fluorescent protein is optimal for primary screening and that automated electrophysiology of cells stably expressing GlyRs is useful for confirming hits and quantitating the actions of identified compounds. The second aim of this review is to demonstrate how these techniques are used in our laboratory for the purpose of both discovering novel GlyR-active compounds and characterizing their binding sites. We also describe a reliable, cost effective method for transfecting HEK293 cells in single wells of a 384-well plate using nanogram quantities of plasmid DNA.
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Affiliation(s)
- Daniel F Gilbert
- Queensland Brain Institute, The University of Queensland Brisbane, QLD, Australia
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Identification of cholesterol-regulating genes by targeted RNAi screening. Cell Metab 2009; 10:63-75. [PMID: 19583955 DOI: 10.1016/j.cmet.2009.05.009] [Citation(s) in RCA: 152] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2008] [Revised: 04/07/2009] [Accepted: 05/26/2009] [Indexed: 11/24/2022]
Abstract
Elevated plasma cholesterol levels are considered responsible for excess cardiovascular morbidity and mortality. Cholesterol in plasma is tightly controlled by cholesterol within cells. Here, we developed and applied an integrative functional genomics strategy that allows systematic identification of regulators of cellular cholesterol levels. Candidate genes were identified by genome-wide gene-expression profiling of sterol-depleted cells and systematic literature queries. The role of these genes in cholesterol regulation was then tested by targeted siRNA knockdown experiments quantifying cellular cholesterol levels and the efficiency of low-density lipoprotein (LDL) uptake. With this strategy, 20 genes were identified as functional regulators of cellular cholesterol homeostasis. Of these, we describe TMEM97 as SREBP target gene that under sterol-depleted conditions localizes to endo-/lysosomal compartments and binds to LDL cholesterol transport-regulating protein Niemann-Pick C1 (NPC1). Taken together, TMEM97 and other factors described here are promising to yield further insights into how cells control cholesterol levels.
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