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Roelse M, Henquet MGL, Verhoeven HA, de Ruijter NCA, Wehrens R, van Lenthe MS, Witkamp RF, Hall RD, Jongsma MA. Calcium Imaging of GPCR Activation Using Arrays of Reverse Transfected HEK293 Cells in a Microfluidic System. SENSORS 2018; 18:s18020602. [PMID: 29462903 PMCID: PMC5855233 DOI: 10.3390/s18020602] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 02/06/2018] [Accepted: 02/12/2018] [Indexed: 11/16/2022]
Abstract
Reverse-transfected cell arrays in microfluidic systems have great potential to perform large-scale parallel screening of G protein-coupled receptor (GPCR) activation. Here, we report the preparation of a novel platform using reverse transfection of HEK293 cells, imaging by stereo-fluorescence microscopy in a flowcell format, real-time monitoring of cytosolic calcium ion fluctuations using the fluorescent protein Cameleon and analysis of GPCR responses to sequential sample exposures. To determine the relationship between DNA concentration and gene expression, we analyzed cell arrays made with variable concentrations of plasmid DNA encoding fluorescent proteins and the Neurokinin 1 (NK1) receptor. We observed pronounced effects on gene expression of both the specific and total DNA concentration. Reverse transfected spots with NK1 plasmid DNA at 1% of total DNA still resulted in detectable NK1 activation when exposed to its ligand. By varying the GPCR DNA concentration in reverse transfection, the sensitivity and robustness of the receptor response for sequential sample exposures was optimized. An injection series is shown for an array containing the NK1 receptor, bitter receptor TAS2R8 and controls. Both receptors were exposed 14 times to alternating samples of two ligands. Specific responses remained reproducible. This platform introduces new opportunities for high throughput screening of GPCR libraries.
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Affiliation(s)
- Margriet Roelse
- BU Bioscience, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
- Laboratory of Plant Physiology, Wageningen University and Research, 6708 PB Wageningen, The Netherlands.
| | - Maurice G L Henquet
- BU Bioscience, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
| | - Harrie A Verhoeven
- BU Bioscience, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
| | - Norbert C A de Ruijter
- Laboratory of Cell Biology, Wageningen University and Research, 6708 PB Wageningen, The Netherlands.
| | - Ron Wehrens
- BU Bioscience, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
- BU Biometris, Wageningen University and Research, 6708 PB Wageningen, The Netherlands.
| | - Marco S van Lenthe
- BU Biometris, Wageningen University and Research, 6708 PB Wageningen, The Netherlands.
| | - Renger F Witkamp
- Human Nutrition and Health, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands.
| | - Robert D Hall
- BU Bioscience, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
- Laboratory of Plant Physiology, Wageningen University and Research, 6708 PB Wageningen, The Netherlands.
| | - Maarten A Jongsma
- BU Bioscience, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
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Popova AA, Schillo SM, Demir K, Ueda E, Nesterov-Mueller A, Levkin PA. Droplet-Array (DA) Sandwich Chip: A Versatile Platform for High-Throughput Cell Screening Based on Superhydrophobic-Superhydrophilic Micropatterning. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2015; 27:5217-5222. [PMID: 26255809 DOI: 10.1002/adma.201502115] [Citation(s) in RCA: 125] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2015] [Revised: 06/30/2015] [Indexed: 06/04/2023]
Abstract
A droplet-array (DA) sandwich chip is a miniaturized platform for cell-based high-throughput screening. It is based on sandwiching of a glass slide with a preprinted library and a superhydrophobic-superhydrophilic pattern, which consists of thousands of simultaneously formed microdroplets containing cells. The DA sandwich chip allows for one-step cell seeding, simultaneous initiation of screening, and 1000 times less reagent consumption than a regular 96-well plate.
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Affiliation(s)
- Anna A Popova
- Karlsruhe Institute of Technology, Institute of Toxicology and Genetics, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Sebastian M Schillo
- Karlsruhe Institute of Technology, Institute of Microstructure Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Konstantin Demir
- Karlsruhe Institute of Technology, Institute of Toxicology and Genetics, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Erica Ueda
- Karlsruhe Institute of Technology, Institute of Toxicology and Genetics, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - A Nesterov-Mueller
- Karlsruhe Institute of Technology, Institute of Microstructure Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Pavel A Levkin
- Karlsruhe Institute of Technology, Institute of Toxicology and Genetics, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
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3
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Srivastava SK, Ramaneti R, Roelse M, Tong HD, Vrouwe EX, Brinkman AGM, de Smet LCPM, van Rijn CJM, Jongsma MA. A generic microfluidic biosensor of G protein-coupled receptor activation – impedance measurements of reversible morphological changes of reverse transfected HEK293 cells on microelectrodes. RSC Adv 2015. [DOI: 10.1039/c5ra04976h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Flowcell with micro-IDEs (250–500 μm) covered with both stable and reverse transfected cells overexpressing membrane receptors to demonstrate impedance responses to serial injections of analyte.
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Affiliation(s)
- Saurabh K. Srivastava
- Plant Research International
- Wageningen UR
- 6708 PB Wageningen
- The Netherlands
- Laboratory of Organic Chemistry
| | | | - Margriet Roelse
- Plant Research International
- Wageningen UR
- 6708 PB Wageningen
- The Netherlands
| | | | | | - Aldo G. M. Brinkman
- Department of Chemical Engineering
- Delft University of Technology
- 2628 BL Delft
- The Netherlands
- NanoNextNL
| | - Louis C. P. M. de Smet
- Department of Chemical Engineering
- Delft University of Technology
- 2628 BL Delft
- The Netherlands
- NanoNextNL
| | - Cees J. M. van Rijn
- Laboratory of Organic Chemistry
- WageningenUR
- 6703 HB Wageningen
- The Netherlands
- Nanosens B.V
| | - Maarten A. Jongsma
- Plant Research International
- Wageningen UR
- 6708 PB Wageningen
- The Netherlands
- NanoNextNL
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4
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Oh EH, Lee SH, Lee SH, Ko HJ, Park TH. Cell-based high-throughput odorant screening system through visualization on a microwell array. Biosens Bioelectron 2014; 53:18-25. [DOI: 10.1016/j.bios.2013.09.039] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 09/18/2013] [Indexed: 11/25/2022]
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Abstract
In the postgenomic era, DNA and protein arrays are increasing the speed at which knowledge is gathered on gene expression in cells and tissues. At the same time, researchers realize that a miniaturized and parallelized analysis of whole cells may equally expedite the acquisition of data describing cellular properties and function. Researchers are starting to explore means of generating and using cell microarrays to investigate cells at higher throughput. In this initial phase of exploration, cell microarrays are being developed for various cellular analyses including the effects of gene expression, cellular reactions to the biomolecular environment, and profiling of cell surface molecules. This article will provide an overview of different types of eukaryotic cell microarrays described to date, how they are generated, and their fields of application.
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Affiliation(s)
- Brigitte Angres
- Department of Cellular Assay Systems, NMI Natural & Medical Sciences Institute at the University of Tübingen, Markwiesenstr. 55, 72770 Reutlingen, Germany.
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6
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Overview of micro- and nano-technology tools for stem cell applications: micropatterned and microelectronic devices. SENSORS 2012. [PMID: 23202240 PMCID: PMC3522993 DOI: 10.3390/s121115947] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
In the past few decades the scientific community has been recognizing the paramount role of the cell microenvironment in determining cell behavior. In parallel, the study of human stem cells for their potential therapeutic applications has been progressing constantly. The use of advanced technologies, enabling one to mimic the in vivo stem cell microenviroment and to study stem cell physiology and physio-pathology, in settings that better predict human cell biology, is becoming the object of much research effort. In this review we will detail the most relevant and recent advances in the field of biosensors and micro- and nano-technologies in general, highlighting advantages and disadvantages. Particular attention will be devoted to those applications employing stem cells as a sensing element.
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Martins SAM, Trabuco JRC, Monteiro GA, Chu V, Conde JP, Prazeres DMF. Towards the miniaturization of GPCR-based live-cell screening assays. Trends Biotechnol 2012; 30:566-74. [PMID: 22921755 DOI: 10.1016/j.tibtech.2012.07.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Revised: 07/23/2012] [Accepted: 07/24/2012] [Indexed: 01/13/2023]
Abstract
G protein-coupled receptors (GPCRs) play a key role in many physiological or disease-related processes and for this reason are favorite targets of the pharmaceutical industry. Although ~30% of marketed drugs target GPCRs, their potential remains largely untapped. The discovery of new leads calls for the screening of thousands of compounds with high-throughput cell-based assays. Although microtiter plate-based high-throughput screening platforms are well established, microarray and microfluidic technologies hold potential for miniaturization, automation, and biosensor integration that may well redefine the format of GPCR screening assays. This paper reviews the latest research efforts directed to bringing microarray and microfluidic technologies into the realm of GPCR-based, live-cell screening assays.
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Affiliation(s)
- Sofia A M Martins
- IBB-Institute for Biotechnology and Bioengineering, Centre for Biological and Chemical Engineering, Department of Bioengineering, Instituto Superior Técnico, Technical University of Lisbon, 1049-001 Lisbon, Portugal
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Site-specific sonoporation of human melanoma cells at the cellular level using high lateral-resolution ultrasonic micro-transducer arrays. Biosens Bioelectron 2011; 27:25-33. [PMID: 21783355 DOI: 10.1016/j.bios.2011.05.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Revised: 05/09/2011] [Accepted: 05/12/2011] [Indexed: 11/23/2022]
Abstract
We developed a new instrumental method by which human melanoma cells (LU1205) are sonoporated via radiation pressures exerted by highly-confined ultrasonic waves produced by high lateral-resolution ultrasonic micro-transducer arrays (UMTAs). The method enables cellular-level site-specific sonoporation within the cell monolayer due to UMTAs and can be applicable in the delivery of drugs and gene products in cellular assays. In this method, cells are seeded on the biochip that employs UMTAs for high spatial resolution and specificity. UMTAs are driven by 30-MHz sinusoidal signals and the resulting radiation pressures induce sonoporation in the targeted cells. The sonoporation degree and the effective lateral resolution of UMTAs are determined by performing fluorescent microscopy and analysis of carboxylic-acid-derivatized CdSe/ZnS quantum dots passively transported into the cells. Models representing the transducer-generated ultrasound radiation pressure, the ultrasound-inflicted cell membrane wound, and the transmembrane transport through the wound are developed to determine the ultrasound-pressure-dependent wound size and enhanced cellular uptake of nanoparticles. Model-based calculations show that the effective wound size and cellular uptake of nanoparticles increase linearly with increasing ultrasound pressure (i.e., at applied radiation pressures of 0.21, 0.29, and 0.40 MPa, the ultrasound-induced initial effective wound radii are 150, 460, and 650 nm, respectively, and the post-sonoporation intracellular quantum-dot concentrations are 7.8, 22.8, and 29.9 nM, respectively) and the threshold pressure required to induce sonoporation in LU1205 cells is ∼0.12 MPa.
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9
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Abstract
Cell-based microarrays were first described by Ziauddin and Sabatini in 2001 as a novel method for performing high-throughput screens of gene function. They reported a technique whereby expression vectors containing the open reading frame (ORF) of human genes were printed onto glass microscope slides to form a microarray. Transfection reagents were added pre- or post-spotting and cells grown over the surface of the array. They demonstrated that cells growing in the immediate vicinity of the expression vectors underwent 'reverse transfection' and that subsequent alterations in cell function could then be detected by secondary assays performed on the array. Subsequent publications have adapted the technique to a variety of applications and have also shown that the approach works when arrays are fabricated using siRNAs and compounds. The potential of this method for performing analyses of gene function and identification of novel therapeutic agents has now been clearly demonstrated. Current efforts are focused on improving and harnessing this technology for high-throughput screening applications.
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Affiliation(s)
- Ella Palmer
- Clinical Sciences Centre, Hammersmith Hospital, London, UK.
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10
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Palmer E, Freeman TC. Large-scale cell-based microarrays and their use with HEK293T cells and downstream apoptotic assays. Methods Mol Biol 2011; 706:27-40. [PMID: 21104052 DOI: 10.1007/978-1-61737-970-3_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Cell-based microarrays are a powerful technology platform for performing high-throughput screens of gene function. The approach entails printing expression vectors containing either genes or shRNAs onto a glass microscope slide or 384-well microtitre plate to form an array. These vectors are then packaged in lipid-based transfection reagent, cells grown over the top of the array are transfected and the arrays can then be examined for alterations in cellular function as manifested in localised changes to the cells biochemistry or morphology. We have used this technology for two purposes: to study the sub-cellular localisation of proteins and to perform a large-scale screen for genes that when over-expressed lead to apoptotic cell death. Here we have provided detailed protocols for the large-scale screen and discuss some of the issues associated with this technology.
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Affiliation(s)
- Ella Palmer
- Clinical Sciences Centre, Hammersmith Hospital, London, UK.
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11
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Ozawa A, Lindberg I, Roth B, Kroeze WK. Deorphanization of novel peptides and their receptors. AAPS JOURNAL 2010; 12:378-84. [PMID: 20446073 DOI: 10.1208/s12248-010-9198-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2010] [Accepted: 04/14/2010] [Indexed: 12/31/2022]
Abstract
Peptide hormones and neuropeptides play important roles in endocrine and neural signaling, often using G protein-coupled receptor (GPCR)-mediated signaling pathways. However, the rate of novel peptide discovery has slowed dramatically in recent years. Genomic sequencing efforts have yielded a large number of cDNA sequences that potentially encode novel candidate peptide precursors, as well as hundreds of orphan GPCRs with no known cognate ligands. The complexity of peptide signaling is further highlighted by the requirement for specific posttranslational processing steps, and these must be accomplished in vitro prior to testing newly discovered peptide precursor candidates in receptor assays. In this review, we present historic as well as current approaches to peptide discovery and GPCR deorphanization. We conclude that parallel and combinatorial discovery methods are likely to represent the most fruitful avenues for both peptide discovery as well as for matching the remaining GPCRs with their peptide ligands.
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Affiliation(s)
- Akihiko Ozawa
- Department of Anatomy and Neurobiology, University of Maryland-Baltimore, 20 Penn St. HSFII Rm S251, Baltimore, Maryland 21201, USA
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12
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Resonant Waveguide Grating Biosensor for Microarrays. SPRINGER SERIES ON CHEMICAL SENSORS AND BIOSENSORS 2010. [DOI: 10.1007/978-3-642-02827-4_2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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13
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Gene delivery to cells on a miniaturized multiwell plate for high-throughput gene function analysis. Anal Bioanal Chem 2008; 392:405-8. [DOI: 10.1007/s00216-008-2281-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2008] [Revised: 06/30/2008] [Accepted: 07/02/2008] [Indexed: 11/25/2022]
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14
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Fjeldbo CS, Misund K, Günther CC, Langaas M, Steigedal TS, Thommesen L, Laegreid A, Bruland T. Functional studies on transfected cell microarray analysed by linear regression modelling. Nucleic Acids Res 2008; 36:e97. [PMID: 18628295 PMCID: PMC2528170 DOI: 10.1093/nar/gkn428] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Transfected cell microarray is a promising method for accelerating the functional exploration of the genome, giving information about protein function in the living cell. The microarrays consist of clusters of cells (spots) overexpressing or silencing a particular gene product. The subsequent analysis of the phenotypic consequences of such perturbations can then be detected using cell-based assays. The focus in the present study was to establish an experimental design and a robust analysis approach for fluorescence intensity data, and to address the use of replicates for studying regulation of gene expression with varying complexity and effect size. Our analysis pipeline includes measurement of fluorescence intensities, normalization strategies using negative control spots and internal control plasmids, and linear regression (ANOVA) modelling for estimating biological effects and calculating P-values for comparisons of interests. Our results show the potential of transfected cell microarrays in studying complex regulation of gene expression by enabling measurement of biological responses in cells with overexpression and downregulation of specific gene products, combined with the possibility of assaying the effects of external stimuli. Simulation experiments show that transfected cell microarrays can be used to reliably detect even quantitatively minor biological effects by including several technical and experimental replicates.
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Affiliation(s)
- Christina Saeten Fjeldbo
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.
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15
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Starkuviene V, Pepperkok R, Erfle H. Transfected cell microarrays: an efficient tool for high-throughput functional analysis. Expert Rev Proteomics 2007; 4:479-89. [PMID: 17705706 DOI: 10.1586/14789450.4.4.479] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Transfected cell microarrays are considered to be a breakthrough methodology for high-throughput and high-content functional genomics. Here, recent advances in the cell microarray field are reviewed, along with its potential to increase the speed of determining gene function. These advances, combined with an increasing number and diversity of gene perturbing systems, such as RNAi and ectopic gene expression, provide tools for expanding our understanding of biology at the systems level.
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Affiliation(s)
- Vytaute Starkuviene
- European Molecular Biology Laboratory, Cell Biology & Cell Biophysics Unit, Heidelberg, Germany.
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16
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Yamauchi F, Okada M, Kato K, Jakt LM, Iwata H. Array-based functional screening for genes that regulate vascular endothelial differentiation of Flk1-positive progenitors derived from embryonic stem cells. Biochim Biophys Acta Gen Subj 2007; 1770:1085-97. [PMID: 17532144 DOI: 10.1016/j.bbagen.2007.04.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2006] [Revised: 04/02/2007] [Accepted: 04/06/2007] [Indexed: 10/23/2022]
Abstract
Functional genomics is a central topic of current biological research, where a reverse genetic approach is one of the most promising strategies to discover functions of novel genes. Such an approach requires high-throughput methodologies to assess biological functions for a huge number of genes. We have developed a transfection array that permits parallel introduction of multiple plasmids separately into living cells. The feasibility of this array was examined in an assay system. Eleven genes were over-expressed alone, or in combination in vascular progenitors derived from embryonic stem cells. Endothelial differentiation of the cells was monitored through a stably transformed EGFP reporter construct that is expressed only in endothelial cells. Transcriptional activators that promote endothelial differentiation, such as Ets1 and Sox7, were identified. In addition, the assays also revealed an inhibitory effect on endothelial differentiation by several of the factors. These results demonstrate the feasibility of the transfection array for use in cell-based, high-throughput functional assays.
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Affiliation(s)
- Fumio Yamauchi
- Institute for Frontier Medical Sciences, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
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17
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Castel D, Pitaval A, Debily MA, Gidrol X. Cell microarrays in drug discovery. Drug Discov Today 2007; 11:616-22. [PMID: 16793530 DOI: 10.1016/j.drudis.2006.05.015] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2006] [Revised: 04/24/2006] [Accepted: 05/22/2006] [Indexed: 11/29/2022]
Abstract
There is an increasing need for systematic cell-based assays in a high-throughput screening (HTS) format to analyze the phenotypic consequences of perturbing mammalian cells with drugs, genes, interfering RNA. Taking advantage of the recent progress in microtechnology, new cell microarrays are being developed and applied to a large range of issues in metazoan cells. This article compares different approaches and evaluates their potential use in the drug discovery process. Although still an emerging technology, cell microarrays hold great promise to optimize the efficiency:cost ratio in cell-based HTS.
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Affiliation(s)
- David Castel
- CEA, DSV, DRR, Service de Génomique Fonctionnelle, 2 rue Gaston Crémieux-CP 22, 91057 Evry Cedex, France
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18
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Tian L, Wang P, Guo J, Wang X, Deng W, Zhang C, Fu D, Gao X, Shi T, Ma D. Screening for novel human genes associated with CRE pathway activation with cell microarray. Genomics 2007; 90:28-34. [PMID: 17490851 DOI: 10.1016/j.ygeno.2007.02.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2006] [Revised: 02/02/2007] [Accepted: 02/15/2007] [Indexed: 02/04/2023]
Abstract
In this study, cell microarray technology is used to identify novel human genes associated with CRE pathway activation. By reverse transfection, expression plasmids containing full-length cDNAs were cotransfected with the reporter plasmid pCRE-d2EGFP to monitor the activation of the CRE pathway via enhanced green fluorescence protein (EGFP) expression. Of the 575 predominantly novel genes screened, 22 exhibited relatively higher EGFP fluorescence compared with a negative control. After a functional validation with a dual luciferase reporter system that included both cis- and trans-luciferase assays, 4 of the 22 genes (RNF41, C8orf32, C6orf208, and MEIS3P1) were confirmed as CRE-pathway activators. Western blot analysis revealed that RNF41 can promote CREB phosphorylation. These results demonstrate the successful combination of cell microarray technology with this reporting system and the potential of this tool to characterize functions of novel genes in a highly parallel format.
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Affiliation(s)
- Linjie Tian
- Chinese National Human Genome Center, Beijing, 3-707 North YongChang Road BDA, Beijing 100176, People's Republic of China
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19
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Hook AL, Thissen H, Voelcker NH. Surface manipulation of biomolecules for cell microarray applications. Trends Biotechnol 2006; 24:471-7. [PMID: 16919345 DOI: 10.1016/j.tibtech.2006.08.001] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2006] [Revised: 07/12/2006] [Accepted: 08/03/2006] [Indexed: 11/23/2022]
Abstract
Many biological events, such as cellular communication, antigen recognition, tissue repair and DNA linear transfer, are intimately associated with biomolecule interactions at the solid-liquid interface. To facilitate the study and use of these biological events for biodevice and biomaterial applications, a sound understanding of how biomolecules behave at interfaces and a concomitant ability to manipulate biomolecules spatially and temporally at surfaces is required. This is particularly true for cell microarray applications, where a range of biological processes must be duly controlled to maximize the efficiency and throughput of these devices. Of particular interest are transfected-cell microarrays (TCMs), which significantly widen the scope of microarray genomic analysis by enabling the high-throughput analysis of gene function within living cells. This article reviews this current research focus, discussing fundamental and applied research into the spatial and temporal surface manipulation of DNA, proteins and other biomolecules and the implications of this work for TCMs.
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Affiliation(s)
- Andrew L Hook
- School of Chemistry, Physics and Earth Sciences, Flinders University, Adelaide 5001, Australia
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20
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Palmer EL, Miller AD, Freeman TC. Identification and characterisation of human apoptosis inducing proteins using cell-based transfection microarrays and expression analysis. BMC Genomics 2006; 7:145. [PMID: 16768789 PMCID: PMC1525185 DOI: 10.1186/1471-2164-7-145] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2006] [Accepted: 06/12/2006] [Indexed: 11/10/2022] Open
Abstract
Background Cell-based microarrays were first described by Ziauddin and Sabatini in 2001 as a powerful new approach for performing high throughput screens of gene function. An important application of cell-based microarrays is in screening for proteins that modulate gene networks. To this end, cells are grown over the surface of arrays of RNAi or expression reagents. Cells growing in the immediate vicinity of the arrayed reagents are transfected and the arrays can then be scanned for cells showing localised changes in function. Here we describe the construction of a large-scale microarray using expression plasmids containing human genes, its use in screening for genes that induce apoptosis when over-expressed and the characterisation of a number of these genes by following the transcriptional response of cell cultures during their induction of apoptosis. Results High-density cell-based arrays were successfully fabricated using 1,959 un-tagged open reading frames (ORFs) taken from the Mammalian Gene Collection (MGC) in mammalian expression vectors. The arrays were then used to screen for genes inducing apoptosis in Human Embryonic Kidney (HEK293T) cells. Using this approach, 10 genes were clearly identified and confirmed to induce apoptosis. Some of these genes have previously been linked to apoptosis, others not. The mechanism of action of three of the 10 genes were then characterised further by following the transcriptional events associated with apoptosis induction using expression profiling microarrays. This data demonstrates a clear pro-apoptotic transcriptional response in cells undergoing apoptosis and also suggests the use of common apoptotic pathways regardless of the nature of the over-expressed protein triggering cell death. Conclusion This study reports the design and use of the first truly large-scale cell-based microarrays for over-expression studies. Ten genes were confirmed to induce apoptosis, some of which were not previously known to possess this activity. Transcriptome analysis on three of the 10 genes demonstrated their use of similar pathways to invoke apoptosis.
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Affiliation(s)
- Ella L Palmer
- MRC Rosalind Franklin Centre for Genomics Research (RFCGR), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SB, UK
- MRC Laboratory for Molecular Cell Biology and Cell Biology Unit, University College London, Gower Street, London WC1E 6BT, UK
| | - Andrew D Miller
- Imperial College Genetic Therapies Centre, Department of Chemistry, Flowers Building, Armstrong Road, Imperial College London, London SW7 2AZ, UK
| | - Tom C Freeman
- MRC Rosalind Franklin Centre for Genomics Research (RFCGR), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SB, UK
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21
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Abstract
RNA interference (RNAi) refers to post-transcriptional silencing of gene expression as a result of the introduction of double-stranded RNA into cells. The application of RNAi in experimental systems has significantly accelerated elucidation of gene functions. In order to facilitate large-scale functional genomics studies using RNAi, several high-throughput approaches have been developed based on microarray or microwell assays. The recent establishment of large libraries of RNAi reagents combined with a variety of detection assays has further improved the performance of functional genome-wide screens in mammalian cells.
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Affiliation(s)
- M Janitz
- Department Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Fabeckstr. 60-62, 14195 Berlin, Germany.
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22
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Fang Y, Peng J, Ferrie AM, Burkhalter RS. Air-Stable G Protein-Coupled Receptor Microarrays and Ligand Binding Characteristics. Anal Chem 2005; 78:149-55. [PMID: 16383322 DOI: 10.1021/ac0514164] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
This paper described novel strategies to achieve air-stable G protein-coupled receptor (GPCR) microarrays and the uses of the microarrays for ligand profiling. Specifically, GPCR cell membrane fragments were suspended in a buffered solution containing bovine serum albumin (BSA) and disaccharide sucrose or trehalose and used for fabricating GPCR microarrays. During the array fabrication and postfabrication processes, BSA molecules were found to effectively form packed layer(s) surrounding the GPCR membranes immobilized onto the predetermined printing area, thereby stabilizing the membrane microspots. The use of disaccharides was shown to protect the integrity and functionality of GPCR microarrays from the typical deterioration of the membranes when fabricated and stored under dry conditions. To utilize the ability of fluorescence technology for multichannel detection as well as to maximize the capability of GPCR microarrays for multiplexed binding assays, several fluorescently labeled ligands were synthesized and optimized for multiplexing binding assays. A schematic microarray of five GPCRs had been used as a model for characterizing the association and dissociation rate constants of labeled ligands binding to their respective receptors in the microarrays. Interestingly, distinct receptor-ligand interactions exhibited different dependence on the type of pH reagent as well as the species and concentration of cations used in a binding assay buffered solution. The potential mechanisms and implications for the uses of air-stable GPCR microarrays were discussed.
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Affiliation(s)
- Ye Fang
- Biochemical Technologies, Science and Technology Division, Corning Incorporated, Sullivan Park, Corning, New York 14831, USA.
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23
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Osmond RIW, Sheehan A, Borowicz R, Barnett E, Harvey G, Turner C, Brown A, Crouch MF, Dyer AR. GPCR Screening via ERK 1/2: A Novel Platform for Screening G Protein–Coupled Receptors. ACTA ACUST UNITED AC 2005; 10:730-7. [PMID: 16129779 DOI: 10.1177/1087057105277968] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Discovery of novel agonists and antagonists for G protein–coupled receptors (GPCRs) relies heavily on cell-based assays because determination of functional consequences of receptor engagement is often desirable. Currently, there are several key parameters measured to achieve this, including mobilization of intracellular Ca2+ and formation of cyclic adenosine monophosphate or inositol triphosphate. However, no single assay platform is suitable for all situations, and all of the assays have limitations. The authors have developed a new high-throughput homogeneous assay platform for GPCR discovery as an alternative to current assays, which employs detection of phosphorylation of the key signaling molecule p42/44 MAP kinase (ERK 1/2). The authors show that ERK 1/2 is consistently activated in cells stimulated by Gq-coupled GPCRs and provides a new high-throughput platform for screening GPCR drug candidates. The activation of ERK 1/2 in Gq-coupled GPCR systems generates comparable pharmacological data for receptor agonist and antagonist data obtained by other GPCR activation measurement techniques.
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Affiliation(s)
- Ronald I W Osmond
- TGR BioSciences Pty Ltd, 31 Dalgleish Street, Thebarton, SA 5031, Australia
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24
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Abstract
Cell-based microarrays were first described by Ziauddin and Sabatini in 2001 as a novel method for performing high-throughput screens of gene function. In this study, expression vectors containing the open reading frame of human genes were printed onto glass microscope slides to form a microarray. Transfection reagents were added pre- or post-spotting, and cells grown over the surface of the array. They demonstrated that cells growing in the immediate vicinity of the expression vectors underwent ‘reverse transfection’, and that subsequent alterations in cell function could then be detected by secondary assays performed on the array. Subsequent publications have adapted the technique to a variety of applications, and have also shown that the approach works when arrays are fabricated using short interfering RNAs and compounds. The potential of this method for performing analyses of gene function and for identifying novel therapeutic agents has been clearly demonstrated, and current efforts are focused on improving and harnessing this technology for high-throughput screening applications.
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Affiliation(s)
- Ella Palmer
- MRC Rosalind Franklin Centre for Genomics Research (RFCGR), Wellcome Trust Genome Campus, Hinxton, Cambridge. CB10 1SB, UK
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25
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Wheeler DB, Carpenter AE, Sabatini DM. Cell microarrays and RNA interference chip away at gene function. Nat Genet 2005; 37 Suppl:S25-30. [PMID: 15920526 DOI: 10.1038/ng1560] [Citation(s) in RCA: 181] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The recent development of cell microarrays offers the potential to accelerate high-throughput functional genetic studies. The widespread use of RNA interference (RNAi) has prompted several groups to fabricate RNAi cell microarrays that make possible discrete, in-parallel transfection with thousands of RNAi reagents on a microarray slide. Though still a budding technology, RNAi cell microarrays promise to increase the efficiency, economy and ease of genome-wide RNAi screens in metazoan cells.
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Affiliation(s)
- Douglas B Wheeler
- Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Department of Biology, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA
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26
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Abstract
Image-based screening (IBS) has proven itself with whole-well assays in which throughput and assay miniaturization are priorities. Recent interest, however, has centered upon the use of automated imaging technology to conduct assays at subcellular resolution. These in vitro assays have the potential to increase lead quality at early stages in drug discovery. Subcellular IBS is not yet mature and, although some assays provide reliable data at reasonable throughput, many others have yet to demonstrate robust application. Developments in image acquisition, analysis and informatics technologies are ongoing and are expected to broaden the usefulness of subcellular IBS.
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Affiliation(s)
- Peter Ramm
- Invicta Research Inc., 290 Riverview Boulevard, St Catharines, ON L2T 3N4, Canada.
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27
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Abstract
In this chapter we describe protocols for reverse transfection to generate mammalian cell arrays for systematic gene knock-downs by RNAi or knock-ins by ectopic cDNA expression. The method is suitable for high content screening microscopy at a high spatial and temporal resolution allowing even time-lapse analysis of hundreds of samples in parallel.
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Affiliation(s)
- Holger Erfle
- Cell Biology and Cell Biophysics Program, European Molecular Biology Laboratory, Heidelberg, Germany
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28
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Abstract
A recently established transfected cell array (TCA) technology has opened new experimental dimensions in the field of functional genomics. Cell arrays allow for transfection of several thousands different DNA molecules in microarray format. The effects of overexpression of hundreds of proteins on cellular physiology can be observed in a single experiment. The TCA technique has also found its application in RNA interference (RNAi) research. Small interfering RNAs (siRNA) as well as plasmid expressing short hairpin RNAs can be transferred into the cells through the process of reverse transfection. The silencing of numerous genes in spatially separated manner can be thus monitored. This review will provide an overview on current concepts concerning combination of cell array and RNAi for high-throughput loss-of-function studies.
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Affiliation(s)
- Dominique Vanhecke
- Max Planck Institute for Molecular Genetics, Department Vertebrate Genomics, Fabeckstr. 60-62, Berlin 14195, Germany
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