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Khalef L, Lydia R, Filicia K, Moussa B. Cell viability and cytotoxicity assays: Biochemical elements and cellular compartments. Cell Biochem Funct 2024; 42:e4007. [PMID: 38593323 DOI: 10.1002/cbf.4007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 03/01/2024] [Accepted: 03/29/2024] [Indexed: 04/11/2024]
Abstract
Cell viability and cytotoxicity assays play a crucial role in drug screening and evaluating the cytotoxic effects of various chemicals. The quantification of cell viability and proliferation serves as the cornerstone for numerous in vitro assays that assess cellular responses to external factors. In the last decade, several studies have developed guidelines for defining and interpreting cell viability and cytotoxicity based on morphological, biochemical, and functional perspectives. As this domain continues to experience ongoing growth, revealing new mechanisms orchestrating diverse cell cytotoxicity pathways, we suggest a revised classification for multiple assays employed in evaluating cell viability and cell death. This classification is rooted in the cellular compartment and/or biochemical element involved, with a specific focus on mechanistic and essential aspects of the process. The assays are founded on diverse cell functions, encompassing metabolic activity, enzyme activity, cell membrane permeability and integrity, adenosine 5'-triphosphate content, cell adherence, reduction equivalents, dye inclusion or exclusion, constitutive protease activity, colony formation, DNA fragmentation and nuclear splitting. These assays present straightforward, reliable, sensitive, reproducible, cost-effective, and high-throughput approaches for appraising the effects of newly formulated chemotherapeutic biomolecules on the cell survival during the drug development process.
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Affiliation(s)
- Lefsih Khalef
- Département de Biochimie et Microbiologie, Laboratoire d'Ecologie, Biotechnologie et Santé, Université Mouloud Mammeri de Tizi ouzou, Tizi Ouzou, Algeria
| | - Radja Lydia
- Département de Biochimie et Microbiologie, Laboratoire d'Ecologie, Biotechnologie et Santé, Université Mouloud Mammeri de Tizi ouzou, Tizi Ouzou, Algeria
| | - Khettar Filicia
- Département de Biochimie et Microbiologie, Laboratoire d'Ecologie, Biotechnologie et Santé, Université Mouloud Mammeri de Tizi ouzou, Tizi Ouzou, Algeria
| | - Berkoud Moussa
- Département de Biochimie et Microbiologie, Laboratoire d'Ecologie, Biotechnologie et Santé, Université Mouloud Mammeri de Tizi ouzou, Tizi Ouzou, Algeria
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2
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Yang J, Hirai Y, Iida K, Ito S, Trumm M, Terada S, Sakai R, Tsuchiya T, Tabata O, Kamei KI. Integrated-gut-liver-on-a-chip platform as an in vitro human model of non-alcoholic fatty liver disease. Commun Biol 2023; 6:310. [PMID: 36959276 PMCID: PMC10036655 DOI: 10.1038/s42003-023-04710-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 03/14/2023] [Indexed: 03/25/2023] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) afflicts a significant percentage of the population; however, no effective treatments have yet been established because of the unsuitability of in vitro assays and animal experimental models. Here, we present an integrated-gut-liver-on-a-chip (iGLC) platform as an in vitro human model of the gut-liver axis (GLA) by co-culturing human gut and liver cell lines interconnected via microfluidics in a closed circulation loop, for the initiation and progression of NAFLD by treatment with free fatty acids (FFAs) for 1 and 7 days, respectively. Co-cultured Caco-2 gut-mimicking cells and HepG2 hepatocyte-like cells demonstrate the protective effects from apoptosis against FFAs treatment, whereas mono-cultured cells exhibit induced apoptosis. Phenotype and gene expression analyses reveal that the FFAs-treated gut and liver cells accumulated intracellular lipid droplets and show an increase in gene expression associated with a cellular response to copper ions and endoplasmic reticulum stress. As an in vitro human GLA model, the iGLC platform may serve as an alternative to animal experiments for investigating the mechanisms of NAFLD.
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Affiliation(s)
- Jiandong Yang
- Department of Micro Engineering, Kyoto University, Kyotodaigaku-Katsura, Nishikyo-ku, Kyoto, 615-8540, Japan
| | - Yoshikazu Hirai
- Department of Micro Engineering, Kyoto University, Kyotodaigaku-Katsura, Nishikyo-ku, Kyoto, 615-8540, Japan.
- Department of Mechanical Engineering and Science, Kyoto University, Kyotodaigaku-Katsura, Nishikyo-ku, Kyoto, 615-8540, Japan.
| | - Kei Iida
- Medical Research Support Center, Graduate School of Medicine, Kyoto University, Yoshida Konoe-cho, Kyoto, 606-8501, Japan
- Faculty of Science and Engineering, Kindai University, 3-4-1 Kowakae, Higashiosaka, Osaka, 577-8502, Japan
| | - Shinji Ito
- Faculty of Science and Engineering, Kindai University, 3-4-1 Kowakae, Higashiosaka, Osaka, 577-8502, Japan
| | - Marika Trumm
- Department of Micro Engineering, Kyoto University, Kyotodaigaku-Katsura, Nishikyo-ku, Kyoto, 615-8540, Japan
- Institute for Integrated Cell-Material Sciences, Kyoto University, Yoshida-Ushinomiya-cho, Sakyo-ku, Kyoto, 606-8501, Japan
- Institute for Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, 69120, Germany
| | - Shiho Terada
- Institute for Integrated Cell-Material Sciences, Kyoto University, Yoshida-Ushinomiya-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Risako Sakai
- Institute for Integrated Cell-Material Sciences, Kyoto University, Yoshida-Ushinomiya-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Toshiyuki Tsuchiya
- Department of Micro Engineering, Kyoto University, Kyotodaigaku-Katsura, Nishikyo-ku, Kyoto, 615-8540, Japan
| | - Osamu Tabata
- Department of Micro Engineering, Kyoto University, Kyotodaigaku-Katsura, Nishikyo-ku, Kyoto, 615-8540, Japan
- Institute for Integrated Cell-Material Sciences, Kyoto University, Yoshida-Ushinomiya-cho, Sakyo-ku, Kyoto, 606-8501, Japan
- Faculty of Engineering/Graduate School of Engineering, Kyoto University of Advanced Science, Gotanda-cho, Yamanouchi, Ukyo-ku, Kyoto, 615-8577, Japan
| | - Ken-Ichiro Kamei
- Institute for Integrated Cell-Material Sciences, Kyoto University, Yoshida-Ushinomiya-cho, Sakyo-ku, Kyoto, 606-8501, Japan.
- Wuya College of Innovation, Shenyang Pharmaceutical University, 110016, Liaoning, China.
- Department of Pharmaceutics, Shenyang Pharmaceutical University, 110016, Liaoning, China.
- Programs of Biology and Bioengineering, Divisions of Science and Engineering, New York University Abu Dhabi, Abu Dhabi, UAE.
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3
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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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4
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Faltus C, Lahnsteiner A, Barrdahl M, Assenov Y, Hüsing A, Bogatyrova O, Laplana M, Johnson T, Muley T, Meister M, Warth A, Thomas M, Plass C, Kaaks R, Risch A. Identification of NHLRC1 as a Novel AKT Activator from a Lung Cancer Epigenome-Wide Association Study (EWAS). Int J Mol Sci 2022; 23:ijms231810699. [PMID: 36142605 PMCID: PMC9505874 DOI: 10.3390/ijms231810699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/07/2022] [Accepted: 09/08/2022] [Indexed: 11/16/2022] Open
Abstract
Changes in DNA methylation identified by epigenome-wide association studies (EWAS) have been recently linked to increased lung cancer risk. However, the cellular effects of these differentially methylated positions (DMPs) are often unclear. Therefore, we investigated top differentially methylated positions identified from an EWAS study. This included a putative regulatory region of NHLRC1. Hypomethylation of this gene was recently linked with decreased survival rates in lung cancer patients. HumanMethylation450 BeadChip array (450K) analysis was performed on 66 lung cancer case-control pairs from the European Prospective Investigation into Cancer and Nutrition Heidelberg lung cancer EWAS (EPIC HD) cohort. DMPs identified in these pre-diagnostic blood samples were then investigated for differential DNA methylation in lung tumor versus adjacent normal lung tissue from The Cancer Genome Atlas (TCGA) and replicated in two independent lung tumor versus adjacent normal tissue replication sets with MassARRAY. The EPIC HD top hypermethylated DMP cg06646708 was found to be a hypomethylated region in multiple data sets of lung tumor versus adjacent normal tissue. Hypomethylation within this region caused increased mRNA transcription of the closest gene NHLRC1 in lung tumors. In functional assays, we demonstrate attenuated proliferation, viability, migration, and invasion upon NHLRC1 knock-down in lung cancer cells. Furthermore, diminished AKT phosphorylation at serine 473 causing expression of pro-apoptotic AKT-repressed genes was detected in these knock-down experiments. In conclusion, this study demonstrates the powerful potential for discovery of novel functional mechanisms in oncogenesis based on EWAS DNA methylation data. NHLRC1 holds promise as a new prognostic biomarker for lung cancer survival and prognosis, as well as a target for novel treatment strategies in lung cancer patients.
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Affiliation(s)
- Christian Faltus
- Division of Cancer Epigenomics, DKFZ–German Cancer Research Center, 69120 Heidelberg, Germany
- Division of Cancer (Epi-)Genetics, Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria
| | - Angelika Lahnsteiner
- Division of Cancer (Epi-)Genetics, Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria
- Cancer Cluster Salzburg, 5020 Salzburg, Austria
| | - Myrto Barrdahl
- Division of Cancer Epidemiology, DKFZ-German Cancer Research Center, 69120 Heidelberg, Germany
| | - Yassen Assenov
- Division of Cancer Epigenomics, DKFZ–German Cancer Research Center, 69120 Heidelberg, Germany
| | - Anika Hüsing
- Division of Cancer Epidemiology, DKFZ-German Cancer Research Center, 69120 Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), 69120 Heidelberg, Germany
| | - Olga Bogatyrova
- Division of Cancer Epigenomics, DKFZ–German Cancer Research Center, 69120 Heidelberg, Germany
| | - Marina Laplana
- Division of Cancer Epigenomics, DKFZ–German Cancer Research Center, 69120 Heidelberg, Germany
- Departament de Ciències Mèdiques Bàsiques, Universitat de Lleida, 25198 Lleida, Spain
| | - Theron Johnson
- Division of Cancer Epidemiology, DKFZ-German Cancer Research Center, 69120 Heidelberg, Germany
| | - Thomas Muley
- Translational Lung Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), 69120 Heidelberg, Germany
- Thoraxklinik at University Hospital Heidelberg, University of Heidelberg, 69126 Heidelberg, Germany
| | - Michael Meister
- Translational Lung Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), 69120 Heidelberg, Germany
- Thoraxklinik at University Hospital Heidelberg, University of Heidelberg, 69126 Heidelberg, Germany
| | - Arne Warth
- Translational Lung Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), 69120 Heidelberg, Germany
- Institute of Pathology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Michael Thomas
- Translational Lung Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), 69120 Heidelberg, Germany
- Thoraxklinik at University Hospital Heidelberg, University of Heidelberg, 69126 Heidelberg, Germany
| | - Christoph Plass
- Division of Cancer Epigenomics, DKFZ–German Cancer Research Center, 69120 Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), 69120 Heidelberg, Germany
| | - Rudolf Kaaks
- Division of Cancer Epidemiology, DKFZ-German Cancer Research Center, 69120 Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), 69120 Heidelberg, Germany
| | - Angela Risch
- Division of Cancer Epigenomics, DKFZ–German Cancer Research Center, 69120 Heidelberg, Germany
- Division of Cancer (Epi-)Genetics, Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria
- Cancer Cluster Salzburg, 5020 Salzburg, Austria
- Translational Lung Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), 69120 Heidelberg, Germany
- Correspondence: ; Tel.: +43-662-8044-7220
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5
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Pai VP, Cooper BG, Levin M. Screening Biophysical Sensors and Neurite Outgrowth Actuators in Human Induced-Pluripotent-Stem-Cell-Derived Neurons. Cells 2022; 11:cells11162470. [PMID: 36010547 PMCID: PMC9406775 DOI: 10.3390/cells11162470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 07/26/2022] [Accepted: 08/04/2022] [Indexed: 11/16/2022] Open
Abstract
All living cells maintain a charge distribution across their cell membrane (membrane potential) by carefully controlled ion fluxes. These bioelectric signals regulate cell behavior (such as migration, proliferation, differentiation) as well as higher-level tissue and organ patterning. Thus, voltage gradients represent an important parameter for diagnostics as well as a promising target for therapeutic interventions in birth defects, injury, and cancer. However, despite much progress in cell and molecular biology, little is known about bioelectric states in human stem cells. Here, we present simple methods to simultaneously track ion dynamics, membrane voltage, cell morphology, and cell activity (pH and ROS), using fluorescent reporter dyes in living human neurons derived from induced neural stem cells (hiNSC). We developed and tested functional protocols for manipulating ion fluxes, membrane potential, and cell activity, and tracking neural responses to injury and reinnervation in vitro. Finally, using morphology sensor, we tested and quantified the ability of physiological actuators (neurotransmitters and pH) to manipulate nerve repair and reinnervation. These methods are not specific to a particular cell type and should be broadly applicable to the study of bioelectrical controls across a wide range of combinations of models and endpoints.
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Affiliation(s)
- Vaibhav P. Pai
- Allen Discovery Center at Tufts University, Medford, MA 02155, USA
| | - Ben G. Cooper
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Michael Levin
- Allen Discovery Center at Tufts University, Medford, MA 02155, USA
- Correspondence:
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6
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Staufer O, Dietrich F, Rimal R, Schröter M, Fabritz S, Boehm H, Singh S, Möller M, Platzman I, Spatz JP. Bottom-up assembly of biomedical relevant fully synthetic extracellular vesicles. SCIENCE ADVANCES 2021; 7:eabg6666. [PMID: 34516902 PMCID: PMC8442894 DOI: 10.1126/sciadv.abg6666] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Extracellular vesicles (EVs) are fundamental for intercellular communication and influence nearly every process in cell physiology. However, because of their intricate molecular complexity, quantitative knowledge on their signaling mechanisms is missing, particularly impeding their therapeutic application. We used a complementary and quantitative engineering approach based on sequential synthetic bottom-up assembly of fully functional EVs with precisely controlled lipid, protein, and RNA composition. We show that the functionalities of synthetic EVs are analogous to natural EVs and demonstrate their programmable therapeutic administration for wound healing and neovascularization therapy. We apply transcriptome profiling to systematically decode synergistic effects between individual EV constituents, enabling analytical dissection and a fundamental understanding of EV signaling.
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Affiliation(s)
- Oskar Staufer
- Department for Cellular Biophysics, Max Planck Institute for Medical Research, Jahnstraße 29, 69120 Heidelberg, Germany
- Institute for Molecular Systems Engineering (IMSE), Heidelberg University, 69120 Heidelberg, Germany
- Max Planck-Bristol Center for Minimal Biology, University of Bristol, 1 Tankard’s Close, Bristol BS8 1TD, UK
- Max Planck School Matter to Life, Jahnstraße 29, 69120 Heidelberg, Germany
- Corresponding author. (O.S.); (I.P.); (J.P.S.)
| | - Franziska Dietrich
- Department for Cellular Biophysics, Max Planck Institute for Medical Research, Jahnstraße 29, 69120 Heidelberg, Germany
- Institute for Molecular Systems Engineering (IMSE), Heidelberg University, 69120 Heidelberg, Germany
| | - Rahul Rimal
- DWI-Leibniz-Institute for Interactive Materials, Forckenbeckstrasse 50, 52056 Aachen, Germany
| | - Martin Schröter
- Department for Cellular Biophysics, Max Planck Institute for Medical Research, Jahnstraße 29, 69120 Heidelberg, Germany
- Institute for Molecular Systems Engineering (IMSE), Heidelberg University, 69120 Heidelberg, Germany
| | - Sebastian Fabritz
- Department for Chemical Biology, Max Planck Institute for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
| | - Heike Boehm
- Department for Cellular Biophysics, Max Planck Institute for Medical Research, Jahnstraße 29, 69120 Heidelberg, Germany
- Institute for Molecular Systems Engineering (IMSE), Heidelberg University, 69120 Heidelberg, Germany
- Max Planck School Matter to Life, Jahnstraße 29, 69120 Heidelberg, Germany
| | - Smriti Singh
- DWI-Leibniz-Institute for Interactive Materials, Forckenbeckstrasse 50, 52056 Aachen, Germany
| | - Martin Möller
- Max Planck School Matter to Life, Jahnstraße 29, 69120 Heidelberg, Germany
- DWI-Leibniz-Institute for Interactive Materials, Forckenbeckstrasse 50, 52056 Aachen, Germany
| | - Ilia Platzman
- Department for Cellular Biophysics, Max Planck Institute for Medical Research, Jahnstraße 29, 69120 Heidelberg, Germany
- Institute for Molecular Systems Engineering (IMSE), Heidelberg University, 69120 Heidelberg, Germany
- Max Planck-Bristol Center for Minimal Biology, University of Bristol, 1 Tankard’s Close, Bristol BS8 1TD, UK
- Corresponding author. (O.S.); (I.P.); (J.P.S.)
| | - Joachim Pius Spatz
- Department for Cellular Biophysics, Max Planck Institute for Medical Research, Jahnstraße 29, 69120 Heidelberg, Germany
- Institute for Molecular Systems Engineering (IMSE), Heidelberg University, 69120 Heidelberg, Germany
- Max Planck-Bristol Center for Minimal Biology, University of Bristol, 1 Tankard’s Close, Bristol BS8 1TD, UK
- Max Planck School Matter to Life, Jahnstraße 29, 69120 Heidelberg, Germany
- Corresponding author. (O.S.); (I.P.); (J.P.S.)
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Pohan G, Espinosa JA, Chen S, Ang KK, Arkin MR, Markossian S. Multiparametric High-Content Assays to Measure Cell Health and Oxidative Damage as a Model for Drug-Induced Liver Injury. ACTA ACUST UNITED AC 2021; 12:e90. [PMID: 33315311 DOI: 10.1002/cpch.90] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Drug-induced liver injury is an important cause of non-approval in drug development and the withdrawal of already approved drugs from the market. Screening human hepatic cell lines for toxicity has been used extensively to predict drug-induced liver injury in preclinical drug development. Assessing hepatic-cell health with more diverse markers will increase the value of in vitro assays and help predict the mechanism of toxicity. We describe three live cell-based assays using HepG2 cells to measure cell health parameters indicative of hepatotoxicity. The first assay measures cellular ATP levels using luciferase. The second and third assays are multiparametric high-content screens covering a panel of cell health markers including cell count, mitochondrial membrane potential and structure, nuclear morphology, vacuolar density, and reactive oxygen species and glutathione levels. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Measurement of cellular ATP content Basic Protocol 2: High-content analysis assay to assess cell count, mitochondrial membrane potential and structure, and reactive oxygen species Basic Protocol 3: High-content analysis assay to assess nuclear morphology, vacuoles, and glutathione content Support Protocol 1: Subculturing and maintaining HepG2 cells Support Protocol 2: Plating HepG2 cell line Support Protocol 3: Transferring compounds by pin tool Support Protocol 4: Generating dose-response curves.
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Affiliation(s)
- Grace Pohan
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, California
| | - Jether Amos Espinosa
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, California
| | | | - Kenny K Ang
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, California
| | - Michelle R Arkin
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, California
| | - Sarine Markossian
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, California.,Current address: National Center for Advancing Translational Sciences, Rockville, Maryland
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8
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Rauf S, Susapto HH, Kahin K, Alshehri S, Abdelrahman S, Lam JH, Asad S, Jadhav S, Sundaramurthi D, Gao X, Hauser CAE. Self-assembling tetrameric peptides allow in situ 3D bioprinting under physiological conditions. J Mater Chem B 2021; 9:1069-1081. [DOI: 10.1039/d0tb02424d] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Tetrameric peptide-based bioinks allow the printing of 3D cell-laden scaffolds under true physiological conditions avoiding harsh UV or chemical treatment.
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9
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Fröhlich T, Mai C, Bogautdinov RP, Morozkina SN, Shavva AG, Friedrich O, Gilbert DF, Tsogoeva SB. Synthesis of Tamoxifen-Artemisinin and Estrogen-Artemisinin Hybrids Highly Potent Against Breast and Prostate Cancer. ChemMedChem 2020; 15:1473-1479. [PMID: 32374071 PMCID: PMC7496903 DOI: 10.1002/cmdc.202000174] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 05/01/2020] [Indexed: 01/02/2023]
Abstract
In the search for new and effective treatments of breast and prostate cancer, a series of hybrid compounds based on tamoxifen, estrogens, and artemisinin were successfully synthesized and analyzed for their in vitro activities against human prostate (PC-3) and breast cancer (MCF-7) cell lines. Most of the hybrid compounds exhibit a strong anticancer activity against both cancer cell lines - for example, EC50 (PC-3) down to 1.07 μM, and EC50 (MCF-7) down to 2.08 μM - thus showing higher activities than their parent compounds 4-hydroxytamoxifen (afimoxifene, 7; EC50 =75.1 (PC-3) and 19.3 μM (MCF-7)), dihydroartemisinin (2; EC50 =263.6 (PC-3) and 49.3 μM (MCF-7)), and artesunic acid (3; EC50 =195.1 (PC-3) and 32.0 μM (MCF-7)). The most potent compounds were the estrogen-artemisinin hybrids 27 and 28 (EC50 =1.18 and 1.07 μM, respectively) against prostate cancer, and hybrid 23 (EC50 =2.08 μM) against breast cancer. These findings demonstrate the high potential of hybridization of artemisinin and estrogens to further improve their anticancer activities and to produce synergistic effects between linked pharmacophores.
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Affiliation(s)
- Tony Fröhlich
- Organic Chemistry Chair I and Interdisciplinary Center for Molecular Materials (ICMM)Friedrich-Alexander University of Erlangen-NürnbergNikolaus-Fiebiger-Straße 1091058ErlangenGermany
| | - Christina Mai
- Organic Chemistry Chair I and Interdisciplinary Center for Molecular Materials (ICMM)Friedrich-Alexander University of Erlangen-NürnbergNikolaus-Fiebiger-Straße 1091058ErlangenGermany
| | | | | | | | - Oliver Friedrich
- Institute of Medical BiotechnologyFriedrich-Alexander University of Erlangen-NürnbergPaul-Gordan-Straße 391052ErlangenGermany
| | - Daniel F. Gilbert
- Institute of Medical BiotechnologyFriedrich-Alexander University of Erlangen-NürnbergPaul-Gordan-Straße 391052ErlangenGermany
| | - Svetlana B. Tsogoeva
- Organic Chemistry Chair I and Interdisciplinary Center for Molecular Materials (ICMM)Friedrich-Alexander University of Erlangen-NürnbergNikolaus-Fiebiger-Straße 1091058ErlangenGermany
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10
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Volpin V, Michels T, Sorrentino A, Menevse AN, Knoll G, Ditz M, Milenkovic VM, Chen CY, Rathinasamy A, Griewank K, Boutros M, Haferkamp S, Berneburg M, Wetzel CH, Seckinger A, Hose D, Goldschmidt H, Ehrenschwender M, Witzens-Harig M, Szoor A, Vereb G, Khandelwal N, Beckhove P. CAMK1D Triggers Immune Resistance of Human Tumor Cells Refractory to Anti-PD-L1 Treatment. Cancer Immunol Res 2020; 8:1163-1179. [PMID: 32665263 DOI: 10.1158/2326-6066.cir-19-0608] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 03/16/2020] [Accepted: 07/09/2020] [Indexed: 11/16/2022]
Abstract
The success of cancer immunotherapy is limited by resistance to immune checkpoint blockade. We therefore conducted a genetic screen to identify genes that mediated resistance against CTLs in anti-PD-L1 treatment-refractory human tumors. Using PD-L1-positive multiple myeloma cells cocultured with tumor-reactive bone marrow-infiltrating CTL as a model, we identified calcium/calmodulin-dependent protein kinase 1D (CAMK1D) as a key modulator of tumor-intrinsic immune resistance. CAMK1D was coexpressed with PD-L1 in anti-PD-L1/PD-1 treatment-refractory cancer types and correlated with poor prognosis in these tumors. CAMK1D was activated by CTL through Fas-receptor stimulation, which led to CAMK1D binding to and phosphorylating caspase-3, -6, and -7, inhibiting their activation and function. Consistently, CAMK1D mediated immune resistance of murine colorectal cancer cells in vivo The pharmacologic inhibition of CAMK1D, on the other hand, restored the sensitivity toward Fas-ligand treatment in multiple myeloma and uveal melanoma cells in vitro Thus, rapid inhibition of the terminal apoptotic cascade by CAMK1D expressed in anti-PD-L1-refractory tumors via T-cell recognition may have contributed to tumor immune resistance.
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Affiliation(s)
- Valentina Volpin
- Regensburg Center for Interventional Immunology (RCI), University Regensburg, Regensburg, Germany.,German Cancer Research Center (DKFZ), Translational Immunology, Heidelberg, Germany
| | - Tillmann Michels
- Regensburg Center for Interventional Immunology (RCI), University Regensburg, Regensburg, Germany.,German Cancer Research Center (DKFZ), Translational Immunology, Heidelberg, Germany.,iOmx Therapeutics AG, Martinsried/Munich, Germany
| | - Antonio Sorrentino
- Regensburg Center for Interventional Immunology (RCI), University Regensburg, Regensburg, Germany.,German Cancer Research Center (DKFZ), Translational Immunology, Heidelberg, Germany
| | - Ayse N Menevse
- Regensburg Center for Interventional Immunology (RCI), University Regensburg, Regensburg, Germany
| | - Gertrud Knoll
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany
| | - Madlen Ditz
- Regensburg Center for Interventional Immunology (RCI), University Regensburg, Regensburg, Germany
| | - Vladimir M Milenkovic
- Department of Psychiatry and Psychotherapy, Molecular Neurosciences, University of Regensburg, Regensburg, Germany
| | - Chih-Yeh Chen
- Regensburg Center for Interventional Immunology (RCI), University Regensburg, Regensburg, Germany
| | - Anchana Rathinasamy
- Regensburg Center for Interventional Immunology (RCI), University Regensburg, Regensburg, Germany
| | - Klaus Griewank
- Department of Dermatology, University Hospital Essen, West German Cancer Center, University Duisburg-Essen and the German Cancer Consortium, Essen, Germany
| | - Michael Boutros
- German Cancer Research Center (DKFZ), Division Signalling and Functional Genomics, Heidelberg, Germany
| | - Sebastian Haferkamp
- Department of Dermatology, University Hospital Regensburg, Regensburg, Germany
| | - Mark Berneburg
- Department of Dermatology, University Hospital Regensburg, Regensburg, Germany
| | - Christian H Wetzel
- Department of Psychiatry and Psychotherapy, Molecular Neurosciences, University of Regensburg, Regensburg, Germany
| | - Anja Seckinger
- Labor für Myelomforschung, Medizinische Klinik V, Universitätsklinikum Heidelberg, Heidelberg, Germany
| | - Dirk Hose
- Department of Hematology and Immunology, Myeloma Center Brussels, Jette, Belgium
| | - Hartmut Goldschmidt
- Department of Internal Medicine V and National Center of Tumor Diseases (NCT), University Hospital Heidelberg, Heidelberg, Germany
| | - Martin Ehrenschwender
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany
| | - Mathias Witzens-Harig
- Department of Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
| | - Arpad Szoor
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Gyorgy Vereb
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | | | - Philipp Beckhove
- Regensburg Center for Interventional Immunology (RCI), University Regensburg, Regensburg, Germany. .,German Cancer Research Center (DKFZ), Translational Immunology, Heidelberg, Germany.,Department of Hematology, Oncology, Internal Medicine 3, University Hospital Regensburg, Regensburg, Germany
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11
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Xi D, Alter T, Einspanier R, Sharbati S, Gölz G. Campylobacter jejuni genes Cj1492c and Cj1507c are involved in host cell adhesion and invasion. Gut Pathog 2020; 12:8. [PMID: 32064001 PMCID: PMC7011364 DOI: 10.1186/s13099-020-00347-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 01/31/2020] [Indexed: 12/11/2022] Open
Abstract
Background Campylobacter jejuni (C. jejuni) has been assigned as an important food-borne pathogen for human health but many pathogenicity factors of C. jejuni and human host cell responses related to the infection have not yet been adequately clarified. This study aimed to determine further C. jejuni pathogenicity factors and virulence genes based on a random mutagenesis approach. A transposon mutant library of C. jejuni NCTC 11168 was constructed and the ability of individual mutants to adhere to and invade human intestinal epithelial cells was evaluated compared to the wild type. We identified two mutants of C. jejuni possessing altered phenotypes with transposon insertions in the genes Cj1492c and Cj1507c. Cj1492c is annotated as a two-component sensor and Cj1507c is described as a regulatory protein. However, functions of both mutated genes are not clarified so far. Results In comparison to the wild type, Cj::1492c and Cj::1507c showed around 70-80% relative motility and Cj::1492c had around 3-times enhanced adhesion and invasion rates whereas Cj::1507c had significantly impaired adhesive and invasive capability. Moreover, Cj::1492c had a longer lag phase and slower growth rate while Cj::1507c showed similar growth compared to the wild type. Between 5 and 24 h post infection, more than 60% of the intracellular wild type C. jejuni were eliminated in HT-29/B6 cells, however, significantly fewer mutants were able to survive intracellularly. Nevertheless, no difference in host cell viability and induction of the pro-inflammatory chemokine IL-8 were determined between both mutants and the wild type. Conclusion We conclude that genes regulated by Cj1507c have an impact on efficient adhesion, invasion and intracellular survival of C. jejuni in HT-29/B6 cells. Furthermore, potential signal sensing by Cj1492c seems to lead to limiting attachment and hence internalisation of C. jejuni. However, as the intracellular survival capacities are reduced, we suggest that signal sensing by Cj1492c impacts several processes related to pathogenicity of C. jejuni.
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Affiliation(s)
- De Xi
- 1Institute of Veterinary Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Thomas Alter
- 2Institute of Food Safety and Food Hygiene, Freie Universität Berlin, Berlin, Germany
| | - Ralf Einspanier
- 1Institute of Veterinary Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Soroush Sharbati
- 1Institute of Veterinary Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Greta Gölz
- 2Institute of Food Safety and Food Hygiene, Freie Universität Berlin, Berlin, Germany
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12
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Kumari M, Liu CH, Wu WC. Oligochitosan modified albumin as plasmid DNA delivery vector: Endocytic trafficking, polyplex fate, in vivo compatibility. Int J Biol Macromol 2020; 142:492-502. [DOI: 10.1016/j.ijbiomac.2019.09.121] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 09/15/2019] [Accepted: 09/16/2019] [Indexed: 01/12/2023]
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13
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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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14
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Protein moiety in oligochitosan modified vector regulates internalization mechanism and gene delivery: Polyplex characterization, intracellular trafficking and transfection. Carbohydr Polym 2018; 202:143-156. [PMID: 30286987 DOI: 10.1016/j.carbpol.2018.08.131] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 08/13/2018] [Accepted: 08/29/2018] [Indexed: 12/11/2022]
Abstract
Oligochitosan-modified proteins have gained attention as efficient non-viral vectors for gene delivery. However, little information exists if protein moieties can serve as an important role for internalization and endosome escape ability of the genetic material. To explore this issue, we designed two cationic oligochitosan-modified vectors that consist of different proteins, namely a hydrophobic plant protein (zein) and a hydrophilic animal protein (ovalbumin (OVA)) to deliver pDNA to epithelial cell line CHO-K1 and HEK 293 T. These cationic vectors were systematically characterized by molecular weight, infrared (IR) structural analysis, transmission electron microscopy (TEM) morphology, and surface charge. A remarkable impact of protein moieties was observed on physiochemical properties of the developed vectors. Oligochitosan-modified zein containing hydrophobic protein exhibited high buffering capacity and excellent DNA binding ability compared to the oligochitosan-modified OVA. The data on transfection in the presence of endocytic inhibitors indicated that the caveolae-mediated pathway (CvME) played a key role in the internalization of the zein-based polyplex. However, the OVA-based polyplex was internalized in CHO-K1 cells via CvME and in HEK 293 T cells via the lipid-mediated pathway. Moreover, oligochitosan-modified zein exhibited lower cytotoxicity, greater lysosomal escape ability, better plasmid stability, and better transfection efficiency than the oligochitosan-modified OVA. This study offers a facile procedure for the synthesis of cationic vectors and elucidates the relationship that exists between protein moieties and transfection activity, thus providing an alternative, non-viral platform for the gene delivery.
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15
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Scheeder C, Heigwer F, Boutros M. Machine learning and image-based profiling in drug discovery. CURRENT OPINION IN SYSTEMS BIOLOGY 2018; 10:43-52. [PMID: 30159406 PMCID: PMC6109111 DOI: 10.1016/j.coisb.2018.05.004] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The increase in imaging throughput, new analytical frameworks and high-performance computational resources open new avenues for data-rich phenotypic profiling of small molecules in drug discovery. Image-based profiling assays assessing single-cell phenotypes have been used to explore mechanisms of action, target efficacy and toxicity of small molecules. Technological advances to generate large data sets together with new machine learning approaches for the analysis of high-dimensional profiling data create opportunities to improve many steps in drug discovery. In this review, we will discuss how recent studies applied machine learning approaches in functional profiling workflows with a focus on chemical genetics. While their utility in image-based screening and profiling is predictably evident, examples of novel insights beyond the status quo based on the applications of machine learning approaches are just beginning to emerge. To enable discoveries, future studies also need to develop methodologies that lower the entry barriers to high-throughput profiling experiments by streamlining image-based profiling assays and providing applications for advanced learning technologies such as easy to deploy deep neural networks.
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Affiliation(s)
| | | | - Michael Boutros
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Heidelberg University, Department of Cell and Molecular Biology, Medical Faculty Mannheim, D-69120 Heidelberg, Germany
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16
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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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17
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Heigwer F, Port F, Boutros M. RNA Interference (RNAi) Screening in Drosophila. Genetics 2018; 208:853-874. [PMID: 29487145 PMCID: PMC5844339 DOI: 10.1534/genetics.117.300077] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 09/28/2017] [Indexed: 12/22/2022] Open
Abstract
In the last decade, RNA interference (RNAi), a cellular mechanism that uses RNA-guided degradation of messenger RNA transcripts, has had an important impact on identifying and characterizing gene function. First discovered in Caenorhabditis elegans, RNAi can be used to silence the expression of genes through introduction of exogenous double-stranded RNA into cells. In Drosophila, RNAi has been applied in cultured cells or in vivo to perturb the function of single genes or to systematically probe gene function on a genome-wide scale. In this review, we will describe the use of RNAi to study gene function in Drosophila with a particular focus on high-throughput screening methods applied in cultured cells. We will discuss available reagent libraries and cell lines, methodological approaches for cell-based assays, and computational methods for the analysis of high-throughput screens. Furthermore, we will review the generation and use of genome-scale RNAi libraries for tissue-specific knockdown analysis in vivo and discuss the differences and similarities with the use of genome-engineering methods such as CRISPR/Cas9 for functional analysis.
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Affiliation(s)
- Florian Heigwer
- Division of Signaling and Functional Genomics, German Cancer Research Center, and Department of Cell and Molecular Biology, Heidelberg University, Medical Faculty Mannheim, D-69120, Germany
| | - Fillip Port
- Division of Signaling and Functional Genomics, German Cancer Research Center, and Department of Cell and Molecular Biology, Heidelberg University, Medical Faculty Mannheim, D-69120, Germany
| | - Michael Boutros
- Division of Signaling and Functional Genomics, German Cancer Research Center, and Department of Cell and Molecular Biology, Heidelberg University, Medical Faculty Mannheim, D-69120, Germany
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18
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Menzner AK, Gilbert DF. A Protocol for In Vitro High-Throughput Chemical Susceptibility Screening in Differentiating NT2 Stem Cells. Methods Mol Biol 2018; 1601:61-70. [PMID: 28470517 DOI: 10.1007/978-1-4939-6960-9_5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The incidence of neurological diseases including learning and developmental disorders has increased in recent years. Concurrently, the number and volume of worldwide registered and traded chemicals have also increased. There is a broad consensus that the developing brain is particularly sensitive to damage by chemicals and that evaluation of chemicals for developmental toxicity or neurotoxicity is critical to human health. Human pluripotent embryonal carcinoma (NTERA-2 or NT2) cells are increasingly considered as a suitable model for in vitro developmental toxicity and neurotoxicity (DT/DNT) studies as they undergo neuronal differentiation upon stimulation with retinoic acid (RA) and allow toxicity assessment at different stages of maturation. Here we describe a protocol for cell fitness screening in differentiating NT2 cells based on the analysis of intracellular ATP levels allowing for the identification of chemicals which are potentially harmful to the developing brain. The described method is suitable to be adapted to low-, medium-, and high-throughput screening and allows multiplexing with other cell fitness indicators. While the presented protocol focuses on cell fitness screening in human pluripotent stem cells it may also be applied to other in vitro models.
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Affiliation(s)
- Ann-Katrin Menzner
- Department of Internal Medicine 5, University Medical Center Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Daniel F Gilbert
- Friedrich-Alexander University (FAU) Erlangen-Nürnberg, Institute of Medical Biotechnology, Paul-Gordan-Street 3, 91052, Erlangen, Germany.
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19
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Chen YC, Chiu WT, Chang C, Wu PC, Tu TY, Lin HP, Chang HC. Chemo-photothermal effects of doxorubicin/silica–carbon hollow spheres on liver cancer. RSC Adv 2018; 8:36775-36784. [PMID: 35558959 PMCID: PMC9089277 DOI: 10.1039/c8ra08538b] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 10/19/2018] [Indexed: 01/20/2023] Open
Abstract
Chemo-photothermal therapy, which exhibits synergistic effects, is more effective than either of the treatments administered alone because of its superior ability to target and destroy cancer cells. An anti-cancer compound (doxorubicin, DOX) was embedded in silica–carbon hollow spheres (SCHSs) using heat and vacuum to integrate multi-therapeutic effects onto one platform and subsequently improve the anti-cancer efficacy. SCHSs were synthesized via a surface activation method and its highly porous surface enhanced the loading content of the desired drug. SCHSs are an infrared photothermal material that can destroy targeted cells by heating under near-infrared (NIR) laser illumination at 808 nm. NIR laser illumination also enhances DOX release from SCHSs to increase the anti-cancer efficiency of DOX–loaded SCHSs (DOX–SCHSs) in both two-dimensional and three-dimensional multicellular tumor spheroid cultures. SCHSs exhibited high heat-generating ability and pH-responsive drug delivery. In conclusion, this study demonstrated that DOX–SCHSs represent a potential tool for chemo-photothermal therapy due to its photothermal effects. Thus, our findings imply that the high cancer cell killing efficiency of DOX–SCHSs induced by NIR illumination can be used for the treatment of tumors. SCHSs were applied as vectors for drug delivery and thermal production under NIR laser irradiation. DOX-loaded SCHSs conjugated with ConA were found to kill liver cancer cells efficiently.![]()
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Affiliation(s)
- Ying-Chi Chen
- Department of Biomedical Engineering
- National Cheng Kung University
- Taiwan
| | - Wen-Tai Chiu
- Department of Biomedical Engineering
- National Cheng Kung University
- Taiwan
- Medical Device Innovation Center
- National Cheng Kung University
| | - Chin Chang
- Department of Chemistry
- National Cheng Kung University
- Taiwan
| | - Ping-Ching Wu
- Department of Biomedical Engineering
- National Cheng Kung University
- Taiwan
- Medical Device Innovation Center
- National Cheng Kung University
| | - Ting-Yuan Tu
- Department of Biomedical Engineering
- National Cheng Kung University
- Taiwan
- Medical Device Innovation Center
- National Cheng Kung University
| | - Hong-Ping Lin
- Department of Chemistry
- National Cheng Kung University
- Taiwan
- Center for Micro/Nano Science and Technology Research
- National Cheng Kung University
| | - Hsien-Chang Chang
- Department of Biomedical Engineering
- National Cheng Kung University
- Taiwan
- Medical Device Innovation Center
- National Cheng Kung University
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20
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Abstract
High-throughput cell viability assays are broadly used in RNAi and small molecule screening experiments to identify compounds that selectively kill cancer cells or as counter screens to exclude the compounds that have a generic effect on cell growth. While there are several assaying techniques available, cellular fitness is often assessed on the basis of one single and often rather indirect physiological indicator. This can lead to inconsistencies and poor correspondence between cell viability screening experiments, conducted under comparable conditions but with different viability indicators. Multiplexing, i.e., the combination of different individual assaying techniques in one experiment and subsequent comparative analysis of multiparametric data can decrease inter-assay variability and increase dataset concordance. Here, we describe a protocol for a multiplexing approach for high-throughput cell viability screening to address the issues encountered in the classical strategy using a single fitness indicator described above. The method combines a biochemical, luminescence-based approach and two fluorescence-based assay types. The biochemical method assesses cellular fitness by quantifying intracellular ATP concentration. Calcein labeling reflects cell fitness through membrane integrity and indirect measurement of ATP-dependent enzymatic esterase activity. Hoechst DNA stain correlates cell fitness with cellular DNA content. The presented multiplexing approach is suitable for low, medium and high-throughput screening and has the potential to decrease inter-assay variability and increase dataset concordance as well as reproducibility of experimental results.
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21
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Two low complexity ultra-high throughput methods to identify diverse chemically bioactive molecules using Saccharomyces cerevisiae. Microbiol Res 2017; 199:10-18. [DOI: 10.1016/j.micres.2017.02.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 02/17/2017] [Accepted: 02/19/2017] [Indexed: 11/21/2022]
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22
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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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23
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Canal F, Anthony E, Lescure A, Del Nery E, Camonis J, Perez F, Ragazzon B, Perret C. A kinome siRNA screen identifies HGS as a potential target for liver cancers with oncogenic mutations in CTNNB1. BMC Cancer 2015; 15:1020. [PMID: 26715116 PMCID: PMC4696130 DOI: 10.1186/s12885-015-2037-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 12/20/2015] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Aberrant activation of the Wnt/β-catenin pathway is a major and frequent event in liver cancer, but inhibition of oncogenic β-catenin signaling has proven challenging. The identification of genes that are synthetically lethal in β-catenin-activated cancer cells would provide new targets for therapeutic drug design. METHODS We transfected the parental HuH6 hepatoblastoma cell line with a doxycycline-inducible shRNA against CTNNB1 (gene coding for β-catenin) to obtain an isogenic cell line pair with or without aberrant β-catenin signaling. Using this hepatoblastoma isogenic cell line pair, we performed a human kinome-wide siRNA screen to identify synthetic lethal interactions with oncogenic CTNNB1. The phenotypic readouts of the screen were cell proliferation, cell cycle arrest and apoptosis, which were assessed by image-based analysis. In addition, apoptosis was assessed by flow cytometric experiments and immunoblotting. The potential synthetic lethal relationship between candidates genes identified in the screen and oncogenic CTNNB1 was also investigated in a different cellular context, a colorectal HCT116 isogenic cell line pair. RESULTS We first determined the experimental conditions that led to the efficient expression of shRNA against CTNNB1 and maximal reduction of β-catenin signaling activity in response to doxycycline treatment. Following high throughput screening in which 687 genes coding for kinases and proteins related to kinases (such as pseudokinases and phosphatases) were targeted, we identified 52 genes required for HuH6 survival. The silencing of five of these genes selectively impaired the viability of HuH6 cells with high β-catenin signaling: HGS, STRADA, FES, BRAF and PKMYT1. Among these candidates, HGS depletion had the strongest inhibitory effect on cell growth and led to apoptosis specifically in HuH6 with high β-catenin activity, while HuH6 with low β-catenin activity were spared. In addition, HGS was identified as a potential synthetic lethal partner of oncogenic CTNNB1 in the HCT116 colorectal isogenic cell line pair. CONCLUSIONS These results demonstrate the existence of crosstalk between β-catenin signaling and HGS. Importantly, HGS depletion specifically affected cells with uncontrolled β-catenin signaling activity in two different types of cancer (Hepatoblastoma HuH6 and colorectal HCT116), and thus may represent a new potential target for novel therapeutic strategies in liver and colorectal cancer.
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Affiliation(s)
- Frédéric Canal
- Department Development, Reproduction and Cancer, INSERM U1016, Institut Cochin, 24, rue du Faubourg Saint-Jacques, 75014, Paris, France. .,CNRS UMR8104, Paris, France. .,Université Paris Descartes, Sorbonne, Paris Cité, France. .,Equipe labellisée Ligue Nationale Contre le Cancer, Paris, France. .,Laboratoire de Génétique et Biologie Cellulaire, Université de Versailles St-Quentin en Yvelines, Montigny le Bretonneux, France.
| | - Elodie Anthony
- Department of Translational Research, the Biophenics High-Content Screening Laboratory, Institut Curie, PSL Research University, Paris, France.
| | - Aurianne Lescure
- Department of Translational Research, the Biophenics High-Content Screening Laboratory, Institut Curie, PSL Research University, Paris, France.
| | - Elaine Del Nery
- Department of Translational Research, the Biophenics High-Content Screening Laboratory, Institut Curie, PSL Research University, Paris, France.
| | - Jacques Camonis
- Department of Translational Research, the Biophenics High-Content Screening Laboratory, Institut Curie, PSL Research University, Paris, France.
| | - Franck Perez
- Department of Translational Research, the Biophenics High-Content Screening Laboratory, Institut Curie, PSL Research University, Paris, France.
| | - Bruno Ragazzon
- Department Development, Reproduction and Cancer, INSERM U1016, Institut Cochin, 24, rue du Faubourg Saint-Jacques, 75014, Paris, France. .,CNRS UMR8104, Paris, France. .,Université Paris Descartes, Sorbonne, Paris Cité, France.
| | - Christine Perret
- Department Development, Reproduction and Cancer, INSERM U1016, Institut Cochin, 24, rue du Faubourg Saint-Jacques, 75014, Paris, France. .,CNRS UMR8104, Paris, France. .,Université Paris Descartes, Sorbonne, Paris Cité, France. .,Equipe labellisée Ligue Nationale Contre le Cancer, Paris, France.
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24
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Khandelwal N, Breinig M, Speck T, Michels T, Kreutzer C, Sorrentino A, Sharma AK, Umansky L, Conrad H, Poschke I, Offringa R, König R, Bernhard H, Machlenkin A, Boutros M, Beckhove P. A high-throughput RNAi screen for detection of immune-checkpoint molecules that mediate tumor resistance to cytotoxic T lymphocytes. EMBO Mol Med 2015; 7:450-63. [PMID: 25691366 PMCID: PMC4403046 DOI: 10.15252/emmm.201404414] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The success of T cell-based cancer immunotherapy is limited by tumor's resistance against killing by cytotoxic T lymphocytes (CTLs). Tumor-immune resistance is mediated by cell surface ligands that engage immune-inhibitory receptors on T cells. These ligands represent potent targets for therapeutic inhibition. So far, only few immune-suppressive ligands have been identified. We here describe a rapid high-throughput siRNA-based screening approach that allows a comprehensive identification of ligands on human cancer cells that inhibit CTL-mediated tumor cell killing. We exemplarily demonstrate that CCR9, which is expressed in many cancers, exerts strong immune-regulatory effects on T cell responses in multiple tumors. Unlike PDL1, which inhibits TCR signaling, CCR9 regulates STAT signaling in T cells, resulting in reduced T-helper-1 cytokine secretion and reduced cytotoxic capacity. Moreover, inhibition of CCR9 expression on tumor cells facilitated immunotherapy of human tumors by tumor-specific T cells in vivo. Taken together, this method allows a rapid and comprehensive determination of immune-modulatory genes in human tumors which, as an entity, represent the ‘immune modulatome’ of cancer.
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Affiliation(s)
- Nisit Khandelwal
- Division of Translational Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marco Breinig
- Division of Signaling and Functional Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany Department of Cell and Molecular Biology, Faculty of Medicine Mannheim, Heidelberg University, Heidelberg, Germany
| | - Tobias Speck
- Division of Translational Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Tillmann Michels
- Division of Translational Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christiane Kreutzer
- Division of Immunogenetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Antonio Sorrentino
- Division of Translational Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ashwini Kumar Sharma
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ludmila Umansky
- Division of Translational Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Heinke Conrad
- Division of Immunogenetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Isabel Poschke
- Department of Molecular Oncology of Gastrointestinal Tumors, German Cancer Research Center (DKFZ) and Division of Pancreas Carcinoma Research, Surgery Clinic of Heidelberg University, Heidelberg, Germany
| | - Rienk Offringa
- Department of Molecular Oncology of Gastrointestinal Tumors, German Cancer Research Center (DKFZ) and Division of Pancreas Carcinoma Research, Surgery Clinic of Heidelberg University, Heidelberg, Germany
| | - Rainer König
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC) Jena University Hospital, Jena, Germany Leibniz Institute for Natural Products Research and Infection Biology, Hans-Knöll-Institute, Jena, Germany
| | - Helga Bernhard
- Department of Hematology/Oncology, Klinikum Darmstadt GmbH, Darmstadt, Germany
| | - Arthur Machlenkin
- Sharett Institute of Oncology, Hadassah-Hebrew University Hospital, Jerusalem, Israel
| | - Michael Boutros
- Division of Signaling and Functional Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany Department of Cell and Molecular Biology, Faculty of Medicine Mannheim, Heidelberg University, Heidelberg, Germany
| | - Philipp Beckhove
- Division of Translational Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany
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25
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Towards in vitro DT/DNT testing: Assaying chemical susceptibility in early differentiating NT2 cells. Toxicology 2015; 338:69-76. [PMID: 26498558 DOI: 10.1016/j.tox.2015.10.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 10/15/2015] [Accepted: 10/15/2015] [Indexed: 11/21/2022]
Abstract
Human pluripotent embryonal carcinoma (NT2) cells are increasingly considered as a suitable model for in vitro toxicity testing, e.g. developmental toxicity and neurotoxicity (DT/DNT) studies, as they undergo neuronal differentiation upon stimulation with retinoic acid (RA) and permit toxicity testing at different stages of maturation. NT2 cells have recently been reported to show specific changes in dielectric resistance profiles during differentiation which can be observed as early as 24h upon RA-stimulation. These observations suggest altered susceptibility to chemicals at an early stage of differentiation. However, chemical susceptibility of early differentiating NT cells has not yet been studied. To address this question, we have established a cell fitness screening assay based on the analysis of intracellular ATP levels and we applied the assay in a large-scale drug screening experiment in NT2 stem cells and early differentiating NT2 cells. Subsequent analysis of ranked fitness phenotypes revealed 19 chemicals with differential toxicity profile in early differentiating NT2 cells. To evaluate whether any of the identified drugs have previously been associated with DT/DNT, we conducted a literature search on the identified molecules and quantified the fraction of chemicals assigned to the FDA (Food and Drug Administration) pregnancy risk categories (PRC) N, A, B, C, D, and X in the hit list and the small molecule library. While the fractions of the categories N and B were decreased (0.81 and 0.35-fold), the classes C, D and X were increased (1.35, 1.47 and 3.27-fold) in the hit list compared to the chemical library. From these data as well as from the literature review, identifying large fractions of chemicals being directly (∼42%) and indirectly associated with DT/DNT (∼32%), we conclude that our method may be beneficial to systematic in vitro-based primary screening for developmental toxicants and neurotoxicants and we propose cell fitness screening in early differentiating NT2 cells as a strategy for evaluating chemical susceptibility at different stages of differentiation to reduce animal testing in the context of the 3Rs.
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26
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Song M, Jeong E, Lee TK, Tsoy Y, Kwon YJ, Yoon S. Analysis of image-based phenotypic parameters for high throughput gene perturbation assays. Comput Biol Chem 2015; 58:192-8. [PMID: 26256799 DOI: 10.1016/j.compbiolchem.2015.07.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 07/14/2015] [Accepted: 07/14/2015] [Indexed: 01/12/2023]
Abstract
Although image-based phenotypic assays are considered a powerful tool for siRNA library screening, the reproducibility and biological implications of various image-based assays are not well-characterized in a systematic manner. Here, we compared the resolution of high throughput assays of image-based cell count and typical cell viability measures for cancer samples. It was found that the optimal plating density of cells was important to obtain maximal resolution in both types of assays. In general, cell counting provided better resolution than the cell viability measure in diverse batches of siRNAs. In addition to cell count, diverse image-based measures were simultaneously collected from a single screening and showed good reproducibility in repetitions. They were classified into a few functional categories according to biological process, based on the differential patterns of hit (i.e., siRNAs) prioritization from the same screening data. The presented systematic analyses of image-based parameters provide new insight to a multitude of applications and better biological interpretation of high content cell-based assays.
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Affiliation(s)
- Mee Song
- Center for Advanced Bioinformatics & Systems Medicine, Sookmyung Women's University, Seoul 140-742, Republic of Korea.
| | - Euna Jeong
- Center for Advanced Bioinformatics & Systems Medicine, Sookmyung Women's University, Seoul 140-742, Republic of Korea.
| | - Tae-Kyu Lee
- Discovery Biology Group, Institute Pasteur Korea, Seongnam-si, Gyeonggi-do 463-400, Republic of Korea.
| | - Yury Tsoy
- Imaging Processing Platform, Institute Pasteur Korea, Seongnam-si, Gyeonggi-do 463-400, Republic of Korea.
| | - Yong-Jun Kwon
- Discovery Biology Group, Institute Pasteur Korea, Seongnam-si, Gyeonggi-do 463-400, Republic of Korea.
| | - Sukjoon Yoon
- Center for Advanced Bioinformatics & Systems Medicine, Sookmyung Women's University, Seoul 140-742, Republic of Korea; Department of Biological Sciences, Sookmyung Women's University, Seoul 140-742, Republic of Korea.
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27
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Chen YC, Chiu WT, Chen JC, Chang CS, Hui-Ching Wang L, Lin HP, Chang HC. The photothermal effect of silica–carbon hollow sphere–concanavalin A on liver cancer cells. J Mater Chem B 2015; 3:2447-2454. [DOI: 10.1039/c5tb00056d] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We used silica–carbon hollow spheres (SCHSs) as material for thermal production under NIR laser irradiation. Concanavalin A (ConA), a lectin, was applied to enhance binding on the cell surface of liver cancer cells. We demonstrated that ConA conjugated SCHSs killed liver cancer cells efficiently.
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Affiliation(s)
- Ying-Chi Chen
- Department of Biomedical Engineering
- National Cheng Kung University
- Tainan 70101
- Taiwan
| | - Wen-Tai Chiu
- Department of Biomedical Engineering
- National Cheng Kung University
- Tainan 70101
- Taiwan
- Medical Device Innovation Center
| | - Jung-Chih Chen
- Institute of Biomedical Engineering
- National Chiao Tung University
- Hsinchu 30010
- Taiwan
| | - Chia-Sheng Chang
- Department of Chemistry
- National Cheng Kung University
- Tainan 70101
- Taiwan
| | - Lily Hui-Ching Wang
- Institute of Molecular and Cellular Biology
- National Tsing Hua University
- Hsinchu 30013
- Taiwan
| | - Hong-Ping Lin
- Department of Chemistry
- National Cheng Kung University
- Tainan 70101
- Taiwan
- Center for Micro/Nano Technology Research
| | - Hsien-Chang Chang
- Department of Biomedical Engineering
- National Cheng Kung University
- Tainan 70101
- Taiwan
- Medical Device Innovation Center
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28
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Saunders DN, Falkenberg KJ, Simpson KJ. High-throughput approaches to measuring cell death. Cold Spring Harb Protoc 2014; 2014:591-601. [PMID: 24890217 DOI: 10.1101/pdb.top072561] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Cell death is integral to developmental and disease processes, and high-throughput screening (HTS) has been instrumental both for understanding biological mechanisms underlying cell death and for discovering novel therapeutic agents targeting these pathways. The various cell death modalities and their distinctive morphological and biochemical features have led to the development of a staggering variety of assays to measure these features, many of which have been adapted to HTS format. Although not all cell death assays are readily amenable to a high-throughput format, the potential power of HTS assays and increasing accessibility to associated technology make it likely that new approaches will continue to emerge. In particular, many recent studies in this field have used multiplex assays and high-content imaging to measure several features concurrently. Here, we discuss a broad array of considerations for designing HTS cell death assays, including some common challenges and pitfalls. We aim to provide a framework for deciding the most appropriate biological readouts, assay strategy and mode, workflow, controls, validation, and bioinformatics.
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Affiliation(s)
- Darren N Saunders
- Cancer Research Program, The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia St. Vincent's Clinical School, University of New South Wales Medicine, Sydney, New South Wales 2000, Australia
| | - Katrina J Falkenberg
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia Department of Pathology, The University of Melbourne, Parkville, Victoria 3052, Australia
| | - Kaylene J Simpson
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia Department of Pathology, The University of Melbourne, Parkville, Victoria 3052, Australia Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria 3052, Australia
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29
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Posimo JM, Unnithan AS, Gleixner AM, Choi HJ, Jiang Y, Pulugulla SH, Leak RK. Viability assays for cells in culture. J Vis Exp 2014:e50645. [PMID: 24472892 DOI: 10.3791/50645] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Manual cell counts on a microscope are a sensitive means of assessing cellular viability but are time-consuming and therefore expensive. Computerized viability assays are expensive in terms of equipment but can be faster and more objective than manual cell counts. The present report describes the use of three such viability assays. Two of these assays are infrared and one is luminescent. Both infrared assays rely on a 16 bit Odyssey Imager. One infrared assay uses the DRAQ5 stain for nuclei combined with the Sapphire stain for cytosol and is visualized in the 700 nm channel. The other infrared assay, an In-Cell Western, uses antibodies against cytoskeletal proteins (α-tubulin or microtubule associated protein 2) and labels them in the 800 nm channel. The third viability assay is a commonly used luminescent assay for ATP, but we use a quarter of the recommended volume to save on cost. These measurements are all linear and correlate with the number of cells plated, but vary in sensitivity. All three assays circumvent time-consuming microscopy and sample the entire well, thereby reducing sampling error. Finally, all of the assays can easily be completed within one day of the end of the experiment, allowing greater numbers of experiments to be performed within short timeframes. However, they all rely on the assumption that cell numbers remain in proportion to signal strength after treatments, an assumption that is sometimes not met, especially for cellular ATP. Furthermore, if cells increase or decrease in size after treatment, this might affect signal strength without affecting cell number. We conclude that all viability assays, including manual counts, suffer from a number of caveats, but that computerized viability assays are well worth the initial investment. Using all three assays together yields a comprehensive view of cellular structure and function.
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Affiliation(s)
- Jessica M Posimo
- Division of Pharmaceutical Sciences, Mylan School of Pharmacy, Duquesne University
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30
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Börner K, Niopek D, Cotugno G, Kaldenbach M, Pankert T, Willemsen J, Zhang X, Schürmann N, Mockenhaupt S, Serva A, Hiet MS, Wiedtke E, Castoldi M, Starkuviene V, Erfle H, Gilbert DF, Bartenschlager R, Boutros M, Binder M, Streetz K, Kräusslich HG, Grimm D. Robust RNAi enhancement via human Argonaute-2 overexpression from plasmids, viral vectors and cell lines. Nucleic Acids Res 2013; 41:e199. [PMID: 24049077 PMCID: PMC3834839 DOI: 10.1093/nar/gkt836] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 08/21/2013] [Accepted: 08/25/2013] [Indexed: 12/31/2022] Open
Abstract
As the only mammalian Argonaute protein capable of directly cleaving mRNAs in a small RNA-guided manner, Argonaute-2 (Ago2) is a keyplayer in RNA interference (RNAi) silencing via small interfering (si) or short hairpin (sh) RNAs. It is also a rate-limiting factor whose saturation by si/shRNAs limits RNAi efficiency and causes numerous adverse side effects. Here, we report a set of versatile tools and widely applicable strategies for transient or stable Ago2 co-expression, which overcome these concerns. Specifically, we engineered plasmids and viral vectors to co-encode a codon-optimized human Ago2 cDNA along with custom shRNAs. Furthermore, we stably integrated this Ago2 cDNA into a panel of standard human cell lines via plasmid transfection or lentiviral transduction. Using various endo- or exogenous targets, we demonstrate the potential of all three strategies to boost mRNA silencing efficiencies in cell culture by up to 10-fold, and to facilitate combinatorial knockdowns. Importantly, these robust improvements were reflected by augmented RNAi phenotypes and accompanied by reduced off-targeting effects. We moreover show that Ago2/shRNA-co-encoding vectors can enhance and prolong transgene silencing in livers of adult mice, while concurrently alleviating hepatotoxicity. Our customizable reagents and avenues should broadly improve future in vitro and in vivo RNAi experiments in mammalian systems.
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Affiliation(s)
- Kathleen Börner
- Department of Infectious Diseases, Virology, Heidelberg University Hospital, Im Neuenheimer Feld 324, D-69120 Heidelberg, Germany, Cluster of Excellence CellNetworks, Heidelberg University, Im Neuenheimer Feld 267, D-69120 Heidelberg, Germany, Department of Medicine III, University Hospital Aachen, Pauwelstrasse 30, D-52074 Aachen, Germany, Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 345, D-69120 Heidelberg, Germany, Division Signaling and Functional Genomics, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany, BioQuant, Heidelberg University, Im Neuenheimer Feld 267, D-69120 Heidelberg, Germany and Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Im Neuenheimer Feld 350, D-69120 Heidelberg, Germany
| | - Dominik Niopek
- Department of Infectious Diseases, Virology, Heidelberg University Hospital, Im Neuenheimer Feld 324, D-69120 Heidelberg, Germany, Cluster of Excellence CellNetworks, Heidelberg University, Im Neuenheimer Feld 267, D-69120 Heidelberg, Germany, Department of Medicine III, University Hospital Aachen, Pauwelstrasse 30, D-52074 Aachen, Germany, Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 345, D-69120 Heidelberg, Germany, Division Signaling and Functional Genomics, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany, BioQuant, Heidelberg University, Im Neuenheimer Feld 267, D-69120 Heidelberg, Germany and Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Im Neuenheimer Feld 350, D-69120 Heidelberg, Germany
| | - Gabriella Cotugno
- Department of Infectious Diseases, Virology, Heidelberg University Hospital, Im Neuenheimer Feld 324, D-69120 Heidelberg, Germany, Cluster of Excellence CellNetworks, Heidelberg University, Im Neuenheimer Feld 267, D-69120 Heidelberg, Germany, Department of Medicine III, University Hospital Aachen, Pauwelstrasse 30, D-52074 Aachen, Germany, Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 345, D-69120 Heidelberg, Germany, Division Signaling and Functional Genomics, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany, BioQuant, Heidelberg University, Im Neuenheimer Feld 267, D-69120 Heidelberg, Germany and Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Im Neuenheimer Feld 350, D-69120 Heidelberg, Germany
| | - Michaela Kaldenbach
- Department of Infectious Diseases, Virology, Heidelberg University Hospital, Im Neuenheimer Feld 324, D-69120 Heidelberg, Germany, Cluster of Excellence CellNetworks, Heidelberg University, Im Neuenheimer Feld 267, D-69120 Heidelberg, Germany, Department of Medicine III, University Hospital Aachen, Pauwelstrasse 30, D-52074 Aachen, Germany, Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 345, D-69120 Heidelberg, Germany, Division Signaling and Functional Genomics, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany, BioQuant, Heidelberg University, Im Neuenheimer Feld 267, D-69120 Heidelberg, Germany and Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Im Neuenheimer Feld 350, D-69120 Heidelberg, Germany
| | - Teresa Pankert
- Department of Infectious Diseases, Virology, Heidelberg University Hospital, Im Neuenheimer Feld 324, D-69120 Heidelberg, Germany, Cluster of Excellence CellNetworks, Heidelberg University, Im Neuenheimer Feld 267, D-69120 Heidelberg, Germany, Department of Medicine III, University Hospital Aachen, Pauwelstrasse 30, D-52074 Aachen, Germany, Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 345, D-69120 Heidelberg, Germany, Division Signaling and Functional Genomics, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany, BioQuant, Heidelberg University, Im Neuenheimer Feld 267, D-69120 Heidelberg, Germany and Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Im Neuenheimer Feld 350, D-69120 Heidelberg, Germany
| | - Joschka Willemsen
- Department of Infectious Diseases, Virology, Heidelberg University Hospital, Im Neuenheimer Feld 324, D-69120 Heidelberg, Germany, Cluster of Excellence CellNetworks, Heidelberg University, Im Neuenheimer Feld 267, D-69120 Heidelberg, Germany, Department of Medicine III, University Hospital Aachen, Pauwelstrasse 30, D-52074 Aachen, Germany, Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 345, D-69120 Heidelberg, Germany, Division Signaling and Functional Genomics, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany, BioQuant, Heidelberg University, Im Neuenheimer Feld 267, D-69120 Heidelberg, Germany and Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Im Neuenheimer Feld 350, D-69120 Heidelberg, Germany
| | - Xian Zhang
- Department of Infectious Diseases, Virology, Heidelberg University Hospital, Im Neuenheimer Feld 324, D-69120 Heidelberg, Germany, Cluster of Excellence CellNetworks, Heidelberg University, Im Neuenheimer Feld 267, D-69120 Heidelberg, Germany, Department of Medicine III, University Hospital Aachen, Pauwelstrasse 30, D-52074 Aachen, Germany, Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 345, D-69120 Heidelberg, Germany, Division Signaling and Functional Genomics, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany, BioQuant, Heidelberg University, Im Neuenheimer Feld 267, D-69120 Heidelberg, Germany and Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Im Neuenheimer Feld 350, D-69120 Heidelberg, Germany
| | - Nina Schürmann
- Department of Infectious Diseases, Virology, Heidelberg University Hospital, Im Neuenheimer Feld 324, D-69120 Heidelberg, Germany, Cluster of Excellence CellNetworks, Heidelberg University, Im Neuenheimer Feld 267, D-69120 Heidelberg, Germany, Department of Medicine III, University Hospital Aachen, Pauwelstrasse 30, D-52074 Aachen, Germany, Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 345, D-69120 Heidelberg, Germany, Division Signaling and Functional Genomics, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany, BioQuant, Heidelberg University, Im Neuenheimer Feld 267, D-69120 Heidelberg, Germany and Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Im Neuenheimer Feld 350, D-69120 Heidelberg, Germany
| | - Stefan Mockenhaupt
- Department of Infectious Diseases, Virology, Heidelberg University Hospital, Im Neuenheimer Feld 324, D-69120 Heidelberg, Germany, Cluster of Excellence CellNetworks, Heidelberg University, Im Neuenheimer Feld 267, D-69120 Heidelberg, Germany, Department of Medicine III, University Hospital Aachen, Pauwelstrasse 30, D-52074 Aachen, Germany, Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 345, D-69120 Heidelberg, Germany, Division Signaling and Functional Genomics, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany, BioQuant, Heidelberg University, Im Neuenheimer Feld 267, D-69120 Heidelberg, Germany and Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Im Neuenheimer Feld 350, D-69120 Heidelberg, Germany
| | - Andrius Serva
- Department of Infectious Diseases, Virology, Heidelberg University Hospital, Im Neuenheimer Feld 324, D-69120 Heidelberg, Germany, Cluster of Excellence CellNetworks, Heidelberg University, Im Neuenheimer Feld 267, D-69120 Heidelberg, Germany, Department of Medicine III, University Hospital Aachen, Pauwelstrasse 30, D-52074 Aachen, Germany, Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 345, D-69120 Heidelberg, Germany, Division Signaling and Functional Genomics, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany, BioQuant, Heidelberg University, Im Neuenheimer Feld 267, D-69120 Heidelberg, Germany and Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Im Neuenheimer Feld 350, D-69120 Heidelberg, Germany
| | - Marie-Sophie Hiet
- Department of Infectious Diseases, Virology, Heidelberg University Hospital, Im Neuenheimer Feld 324, D-69120 Heidelberg, Germany, Cluster of Excellence CellNetworks, Heidelberg University, Im Neuenheimer Feld 267, D-69120 Heidelberg, Germany, Department of Medicine III, University Hospital Aachen, Pauwelstrasse 30, D-52074 Aachen, Germany, Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 345, D-69120 Heidelberg, Germany, Division Signaling and Functional Genomics, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany, BioQuant, Heidelberg University, Im Neuenheimer Feld 267, D-69120 Heidelberg, Germany and Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Im Neuenheimer Feld 350, D-69120 Heidelberg, Germany
| | - Ellen Wiedtke
- Department of Infectious Diseases, Virology, Heidelberg University Hospital, Im Neuenheimer Feld 324, D-69120 Heidelberg, Germany, Cluster of Excellence CellNetworks, Heidelberg University, Im Neuenheimer Feld 267, D-69120 Heidelberg, Germany, Department of Medicine III, University Hospital Aachen, Pauwelstrasse 30, D-52074 Aachen, Germany, Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 345, D-69120 Heidelberg, Germany, Division Signaling and Functional Genomics, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany, BioQuant, Heidelberg University, Im Neuenheimer Feld 267, D-69120 Heidelberg, Germany and Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Im Neuenheimer Feld 350, D-69120 Heidelberg, Germany
| | - Mirco Castoldi
- Department of Infectious Diseases, Virology, Heidelberg University Hospital, Im Neuenheimer Feld 324, D-69120 Heidelberg, Germany, Cluster of Excellence CellNetworks, Heidelberg University, Im Neuenheimer Feld 267, D-69120 Heidelberg, Germany, Department of Medicine III, University Hospital Aachen, Pauwelstrasse 30, D-52074 Aachen, Germany, Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 345, D-69120 Heidelberg, Germany, Division Signaling and Functional Genomics, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany, BioQuant, Heidelberg University, Im Neuenheimer Feld 267, D-69120 Heidelberg, Germany and Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Im Neuenheimer Feld 350, D-69120 Heidelberg, Germany
| | - Vytaute Starkuviene
- Department of Infectious Diseases, Virology, Heidelberg University Hospital, Im Neuenheimer Feld 324, D-69120 Heidelberg, Germany, Cluster of Excellence CellNetworks, Heidelberg University, Im Neuenheimer Feld 267, D-69120 Heidelberg, Germany, Department of Medicine III, University Hospital Aachen, Pauwelstrasse 30, D-52074 Aachen, Germany, Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 345, D-69120 Heidelberg, Germany, Division Signaling and Functional Genomics, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany, BioQuant, Heidelberg University, Im Neuenheimer Feld 267, D-69120 Heidelberg, Germany and Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Im Neuenheimer Feld 350, D-69120 Heidelberg, Germany
| | - Holger Erfle
- Department of Infectious Diseases, Virology, Heidelberg University Hospital, Im Neuenheimer Feld 324, D-69120 Heidelberg, Germany, Cluster of Excellence CellNetworks, Heidelberg University, Im Neuenheimer Feld 267, D-69120 Heidelberg, Germany, Department of Medicine III, University Hospital Aachen, Pauwelstrasse 30, D-52074 Aachen, Germany, Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 345, D-69120 Heidelberg, Germany, Division Signaling and Functional Genomics, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany, BioQuant, Heidelberg University, Im Neuenheimer Feld 267, D-69120 Heidelberg, Germany and Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Im Neuenheimer Feld 350, D-69120 Heidelberg, Germany
| | - Daniel F. Gilbert
- Department of Infectious Diseases, Virology, Heidelberg University Hospital, Im Neuenheimer Feld 324, D-69120 Heidelberg, Germany, Cluster of Excellence CellNetworks, Heidelberg University, Im Neuenheimer Feld 267, D-69120 Heidelberg, Germany, Department of Medicine III, University Hospital Aachen, Pauwelstrasse 30, D-52074 Aachen, Germany, Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 345, D-69120 Heidelberg, Germany, Division Signaling and Functional Genomics, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany, BioQuant, Heidelberg University, Im Neuenheimer Feld 267, D-69120 Heidelberg, Germany and Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Im Neuenheimer Feld 350, D-69120 Heidelberg, Germany
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Virology, Heidelberg University Hospital, Im Neuenheimer Feld 324, D-69120 Heidelberg, Germany, Cluster of Excellence CellNetworks, Heidelberg University, Im Neuenheimer Feld 267, D-69120 Heidelberg, Germany, Department of Medicine III, University Hospital Aachen, Pauwelstrasse 30, D-52074 Aachen, Germany, Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 345, D-69120 Heidelberg, Germany, Division Signaling and Functional Genomics, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany, BioQuant, Heidelberg University, Im Neuenheimer Feld 267, D-69120 Heidelberg, Germany and Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Im Neuenheimer Feld 350, D-69120 Heidelberg, Germany
| | - Michael Boutros
- Department of Infectious Diseases, Virology, Heidelberg University Hospital, Im Neuenheimer Feld 324, D-69120 Heidelberg, Germany, Cluster of Excellence CellNetworks, Heidelberg University, Im Neuenheimer Feld 267, D-69120 Heidelberg, Germany, Department of Medicine III, University Hospital Aachen, Pauwelstrasse 30, D-52074 Aachen, Germany, Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 345, D-69120 Heidelberg, Germany, Division Signaling and Functional Genomics, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany, BioQuant, Heidelberg University, Im Neuenheimer Feld 267, D-69120 Heidelberg, Germany and Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Im Neuenheimer Feld 350, D-69120 Heidelberg, Germany
| | - Marco Binder
- Department of Infectious Diseases, Virology, Heidelberg University Hospital, Im Neuenheimer Feld 324, D-69120 Heidelberg, Germany, Cluster of Excellence CellNetworks, Heidelberg University, Im Neuenheimer Feld 267, D-69120 Heidelberg, Germany, Department of Medicine III, University Hospital Aachen, Pauwelstrasse 30, D-52074 Aachen, Germany, Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 345, D-69120 Heidelberg, Germany, Division Signaling and Functional Genomics, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany, BioQuant, Heidelberg University, Im Neuenheimer Feld 267, D-69120 Heidelberg, Germany and Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Im Neuenheimer Feld 350, D-69120 Heidelberg, Germany
| | - Konrad Streetz
- Department of Infectious Diseases, Virology, Heidelberg University Hospital, Im Neuenheimer Feld 324, D-69120 Heidelberg, Germany, Cluster of Excellence CellNetworks, Heidelberg University, Im Neuenheimer Feld 267, D-69120 Heidelberg, Germany, Department of Medicine III, University Hospital Aachen, Pauwelstrasse 30, D-52074 Aachen, Germany, Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 345, D-69120 Heidelberg, Germany, Division Signaling and Functional Genomics, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany, BioQuant, Heidelberg University, Im Neuenheimer Feld 267, D-69120 Heidelberg, Germany and Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Im Neuenheimer Feld 350, D-69120 Heidelberg, Germany
| | - Hans-Georg Kräusslich
- Department of Infectious Diseases, Virology, Heidelberg University Hospital, Im Neuenheimer Feld 324, D-69120 Heidelberg, Germany, Cluster of Excellence CellNetworks, Heidelberg University, Im Neuenheimer Feld 267, D-69120 Heidelberg, Germany, Department of Medicine III, University Hospital Aachen, Pauwelstrasse 30, D-52074 Aachen, Germany, Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 345, D-69120 Heidelberg, Germany, Division Signaling and Functional Genomics, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany, BioQuant, Heidelberg University, Im Neuenheimer Feld 267, D-69120 Heidelberg, Germany and Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Im Neuenheimer Feld 350, D-69120 Heidelberg, Germany
| | - Dirk Grimm
- Department of Infectious Diseases, Virology, Heidelberg University Hospital, Im Neuenheimer Feld 324, D-69120 Heidelberg, Germany, Cluster of Excellence CellNetworks, Heidelberg University, Im Neuenheimer Feld 267, D-69120 Heidelberg, Germany, Department of Medicine III, University Hospital Aachen, Pauwelstrasse 30, D-52074 Aachen, Germany, Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 345, D-69120 Heidelberg, Germany, Division Signaling and Functional Genomics, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany, BioQuant, Heidelberg University, Im Neuenheimer Feld 267, D-69120 Heidelberg, Germany and Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Im Neuenheimer Feld 350, D-69120 Heidelberg, Germany
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Demir K, Kirsch N, Beretta C, Erdmann G, Ingelfinger D, Moro E, Argenton F, Carl M, Niehrs C, Boutros M. RAB8B Is Required for Activity and Caveolar Endocytosis of LRP6. Cell Rep 2013; 4:1224-34. [DOI: 10.1016/j.celrep.2013.08.008] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2013] [Revised: 07/03/2013] [Accepted: 08/06/2013] [Indexed: 10/26/2022] Open
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Van Reet N, Pyana P, Rogé S, Claes F, Büscher P. Luminescent multiplex viability assay for Trypanosoma brucei gambiense. Parasit Vectors 2013; 6:207. [PMID: 23856321 PMCID: PMC3728213 DOI: 10.1186/1756-3305-6-207] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 07/09/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND New compounds for the treatment of human African trypanosomiasis (HAT) are urgently required. Trypanosoma brucei (T.b.) gambiense is the leading cause of HAT, yet T.b. gambiense is often not the prime target organism in drug discovery. This may be attributed to the difficulties in handling this subspecies and the lack of an efficient viability assay to monitor drug efficacy. METHODS In this study, a T.b. gambiense strain, recently isolated in the D.R. Congo, was made bioluminescent by transfection with Renilla luciferase (RLuc) without altering its in vitro and in vivo growth characteristics. A luminescent multiplex viability assay (LMVA), based on measurement of the Renilla luciferase activity and the ATP content of the cells within the same experiment, was investigated as an alternative to the standard fluorimetric resazurin viability assay for drug sensitivity testing of T.b. gambiense. RESULTS In a 96-well format, the RLuc transfected strain showed a detection limit of 2 × 10(4) cells ml(-1) for the Renilla luciferase measurement and 5 × 10(3) cells ml(-1) for the ATP measurement. Both assays of the LMVA showed linearity up to 10(6) cells ml(-1) and correlated well with the cell density during exponential growth of the long slender bloodstream forms. The LMVA was compared to the fluorimetric resazurin viability assay for drug sensitivity testing of pentamidine, eflornithine, nifurtimox and melarsoprol with both the wild type and the RLuc transfected population. For each drug, the IC50 value of the RLuc population was similar to that of the wild type when determined with either the fluorimetric resazurin method or the LMVA. For eflornithine, nifurtimox and melarsoprol we found no difference between the IC50 values in both viability assays. In contrast, the IC50 value of pentamidine was higher when determined with the fluorimetric resazurin method than in both assays of the LMVA. CONCLUSIONS LMVA has some advantages for viability measurement of T.b. gambiense: it requires less incubation time for viability detection than the fluorimetric resazurin assay and in LMVA, two sensitive and independent viability assays are performed in the same experiment.
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Affiliation(s)
- Nick Van Reet
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.
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Kulak O, Lum L. A multiplexed luciferase-based screening platform for interrogating cancer-associated signal transduction in cultured cells. J Vis Exp 2013:e50369. [PMID: 23852434 DOI: 10.3791/50369] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Genome-scale interrogation of gene function using RNA interference (RNAi) holds tremendous promise for the rapid identification of chemically tractable cancer cell vulnerabilities. Limiting the potential of this technology is the inability to rapidly delineate the mechanistic basis of phenotypic outcomes and thus inform the development of molecularly targeted therapeutic strategies. We outline here methods to deconstruct cellular phenotypes induced by RNAi-mediated gene targeting using multiplexed reporter systems that allow monitoring of key cancer cell-associated processes. This high-content screening methodology is versatile and can be readily adapted for the screening of other types of large molecular libraries.
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Affiliation(s)
- Ozlem Kulak
- Department of Cell Biology, UT Southwestern Medical Center
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Saito T, Tabata Y. Preparation of gelatin hydrogels incorporating small interfering RNA for the controlled release. J Drug Target 2012; 20:864-72. [DOI: 10.3109/1061186x.2012.725170] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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A genome-wide RNA interference screen identifies caspase 4 as a factor required for tumor necrosis factor alpha signaling. Mol Cell Biol 2012; 32:3372-81. [PMID: 22733992 DOI: 10.1128/mcb.06739-11] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Tumor necrosis factor alpha (TNF-α) is a potent inflammatory cytokine secreted upon cellular stress as well as immunological stimuli and is implicated in the pathology of inflammatory diseases and cancer. The therapeutic potential of modifying TNF-α pathway activity has been realized in several diseases, and antagonists of TNF-α have reached clinical applications. While much progress in the understanding of signaling downstream of the TNF-α receptor complex has been made, the compendium of factors required for signal transduction is still not complete. In order to find novel regulators of proinflammatory signaling induced by TNF-α, we conducted a genome-wide small interfering RNA screen in human cells. We identified several new candidate modulators of TNF-α signaling, which were confirmed in independent experiments. Specifically, we show that caspase 4 is required for the induction of NF-κB activity, while it appears to be dispensable for the activation of the Jun N-terminal protein kinase signaling branch. Taken together, our experiments identify caspase 4 as a novel regulator of TNF-α-induced NF-κB signaling that is required for the activation of IκB kinase. We further provide the genome-wide RNA interference data set as a compendium in a format compliant with minimum information about an interfering RNA experiment (MAIRE).
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Abstract
Over the last decade, cell-based screening has become a powerful method in target identification and plays an important role both in basic research and drug discovery. The availability of whole genome sequences and improvements in cell-based screening techniques opened new avenues for high-throughput experiments. Large libraries of RNA interference reagents available for many organisms allow the dissection of broad spectrum of cellular processes. Here, we describe the current state of the large-scale phenotype screening with a focus on cell-based screens. We underline the importance and provide details of screen design, scalability, performance, data analysis, and hit prioritization. Similar to classical high-throughput in vitro screens with defined-target approaches in the past, cell-based screens depend on a successful establishment of robust phenotypic assays, the ability to quantitatively measure phenotypic changes and bioinformatics methods for data analysis, integration, and interpretation.
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Affiliation(s)
- Kubilay Demir
- Division of Signaling and Functional Genomics, Department for Cell and Molecular Biology, German Cancer Research Center (DKFZ), Heidelberg University, Heidelberg, Germany
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