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Jonczyk R, Kurth T, Lavrentieva A, Walter JG, Scheper T, Stahl F. Living Cell Microarrays: An Overview of Concepts. MICROARRAYS (BASEL, SWITZERLAND) 2016; 5:E11. [PMID: 27600077 PMCID: PMC5003487 DOI: 10.3390/microarrays5020011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 05/09/2016] [Accepted: 05/11/2016] [Indexed: 02/06/2023]
Abstract
Living cell microarrays are a highly efficient cellular screening system. Due to the low number of cells required per spot, cell microarrays enable the use of primary and stem cells and provide resolution close to the single-cell level. Apart from a variety of conventional static designs, microfluidic microarray systems have also been established. An alternative format is a microarray consisting of three-dimensional cell constructs ranging from cell spheroids to cells encapsulated in hydrogel. These systems provide an in vivo-like microenvironment and are preferably used for the investigation of cellular physiology, cytotoxicity, and drug screening. Thus, many different high-tech microarray platforms are currently available. Disadvantages of many systems include their high cost, the requirement of specialized equipment for their manufacture, and the poor comparability of results between different platforms. In this article, we provide an overview of static, microfluidic, and 3D cell microarrays. In addition, we describe a simple method for the printing of living cell microarrays on modified microscope glass slides using standard DNA microarray equipment available in most laboratories. Applications in research and diagnostics are discussed, e.g., the selective and sensitive detection of biomarkers. Finally, we highlight current limitations and the future prospects of living cell microarrays.
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Affiliation(s)
- Rebecca Jonczyk
- Institute of Technical Chemistry, Leibniz University of Hannover, Callinstr. 5, Hannover 30167, Germany.
| | - Tracy Kurth
- Institute of Technical Chemistry, Leibniz University of Hannover, Callinstr. 5, Hannover 30167, Germany.
| | - Antonina Lavrentieva
- Institute of Technical Chemistry, Leibniz University of Hannover, Callinstr. 5, Hannover 30167, Germany.
| | - Johanna-Gabriela Walter
- Institute of Technical Chemistry, Leibniz University of Hannover, Callinstr. 5, Hannover 30167, Germany.
| | - Thomas Scheper
- Institute of Technical Chemistry, Leibniz University of Hannover, Callinstr. 5, Hannover 30167, Germany.
| | - Frank Stahl
- Institute of Technical Chemistry, Leibniz University of Hannover, Callinstr. 5, Hannover 30167, Germany.
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Lee HS, Park YY, Cho MY, Chae S, Yoo YS, Kwon MH, Lee CW, Cho H. The chromatin remodeller RSF1 is essential for PLK1 deposition and function at mitotic kinetochores. Nat Commun 2015; 6:7904. [PMID: 26259146 PMCID: PMC4918322 DOI: 10.1038/ncomms8904] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 06/22/2015] [Indexed: 01/04/2023] Open
Abstract
Accumulation of PLK1 at kinetochores is essential for chromosome alignment and segregation; however, the mechanism underlying PLK1 recruitment to kinetochores remains unresolved. The chromatin remodeller RSF1 tightly associates with centromere proteins, but its mitotic function is unknown. Here we show that RSF1 localizes at mitotic kinetochores and directly binds PLK1. RSF1 depletion disrupts localization of PLK1 at kinetochores; the C-terminal fragment of RSF1, which can bind PLK1, is sufficient to restore PLK1 localization. Moreover, CDK1 phosphorylates RSF1 at Ser1375, and this phosphorylation is necessary for PLK1 recruitment. Subsequently, PLK1 phosphorylates RSF1 at Ser1359, stabilizing PLK1 deposition. Importantly, RSF1 depletion mimicks the chromosome misalignment phenotype resulting from PLK1 knockdown; these defects are rescued by RSF1 S1375D or RSF1 S1359D but not RSF1 S1375A, showing a functional link between phosphorylation of RSF1 and chromosome alignment. Together, these data show that RSF1 is an essential centromeric component that recruits PLK1 to kinetochores and plays a crucial role in faithful cell division.
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Affiliation(s)
- Ho-Soo Lee
- Department of Biochemistry, Ajou University School of Medicine, Suwon 443-380, Korea
- Department of Biomedical Sciences, Graduate School of Ajou University, Suwon 443-380, Korea
| | - Yong-Yea Park
- Department of Biochemistry, Ajou University School of Medicine, Suwon 443-380, Korea
| | - Mi-Young Cho
- Department of Biochemistry, Ajou University School of Medicine, Suwon 443-380, Korea
- Department of Biomedical Sciences, Graduate School of Ajou University, Suwon 443-380, Korea
| | - Sunyoung Chae
- Department of Biochemistry, Ajou University School of Medicine, Suwon 443-380, Korea
| | - Young-Suk Yoo
- Department of Biochemistry, Ajou University School of Medicine, Suwon 443-380, Korea
- Department of Biomedical Sciences, Graduate School of Ajou University, Suwon 443-380, Korea
| | - Myung-Hee Kwon
- Department of Biomedical Sciences, Graduate School of Ajou University, Suwon 443-380, Korea
- Department of Microbiology, Ajou University School of Medicine, Suwon 443-380, Korea
| | - Chang-Woo Lee
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon 440-746, Korea
| | - Hyeseong Cho
- Department of Biochemistry, Ajou University School of Medicine, Suwon 443-380, Korea
- Department of Biomedical Sciences, Graduate School of Ajou University, Suwon 443-380, Korea
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Optimizing cell arrays for accurate functional genomics. BMC Res Notes 2012; 5:358. [PMID: 22805280 PMCID: PMC3541979 DOI: 10.1186/1756-0500-5-358] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Accepted: 06/14/2012] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Cellular responses emerge from a complex network of dynamic biochemical reactions. In order to investigate them is necessary to develop methods that allow perturbing a high number of gene products in a flexible and fast way. Cell arrays (CA) enable such experiments on microscope slides via reverse transfection of cellular colonies growing on spotted genetic material. In contrast to multi-well plates, CA are susceptible to contamination among neighboring spots hindering accurate quantification in cell-based screening projects. Here we have developed a quality control protocol for quantifying and minimizing contamination in CA. RESULTS We imaged checkered CA that express two distinct fluorescent proteins and segmented images into single cells to quantify the transfection efficiency and interspot contamination. Compared with standard procedures, we measured a 3-fold reduction of contaminants when arrays containing HeLa cells were washed shortly after cell seeding. We proved that nucleic acid uptake during cell seeding rather than migration among neighboring spots was the major source of contamination. Arrays of MCF7 cells developed without the washing step showed 7-fold lower percentage of contaminant cells, demonstrating that contamination is dependent on specific cell properties. CONCLUSIONS Previously published methodological works have focused on achieving high transfection rate in densely packed CA. Here, we focused in an equally important parameter: The interspot contamination. The presented quality control is essential for estimating the rate of contamination, a major source of false positives and negatives in current microscopy based functional genomics screenings. We have demonstrated that a washing step after seeding enhances CA quality for HeLA but is not necessary for MCF7. The described method provides a way to find optimal seeding protocols for cell lines intended to be used for the first time in CA.
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Fjeldbo CS, Bakke I, Erlandsen SE, Holmseth J, Lægreid A, Sandvik AK, Thommesen L, Bruland T. Gastrin upregulates the prosurvival factor secretory clusterin in adenocarcinoma cells and in oxyntic mucosa of hypergastrinemic rats. Am J Physiol Gastrointest Liver Physiol 2012; 302:G21-33. [PMID: 21995960 DOI: 10.1152/ajpgi.00197.2011] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
We show that the gastric hormone gastrin induces the expression of the prosurvival secretory clusterin (sCLU) in rat adenocarcinoma cells. Clusterin mRNA was still upregulated in the presence of the protein synthesis inhibitor cycloheximide, although at a lower level. This indicates that gastrin induces clusterin transcription independently of de novo protein synthesis but requires de novo protein synthesis of signal transduction pathway components to achieve maximal expression level. Luciferase reporter assay indicates that the AP-1 transcription factor complex is involved in gastrin-mediated activation of the clusterin promoter. Gastrin-induced clusterin expression and subsequent secretion is dependent on sustained treatment, because removal of gastrin after 1-2 h abolished the response. Neutralization of secreted clusterin by a specific antibody abolished the antiapoptotic effect of gastrin on serum starvation-induced apoptosis, suggesting that extracellular clusterin is involved in gastrin-mediated inhibition of apoptosis. The clusterin response to gastrin was validated in vivo in hypergastrinemic rats, showing increased clusterin expression in the oxyntic mucosa, as well as higher levels of clusterin in plasma. In normal rat oxyntic mucosa, clusterin protein was strongly expressed in chromogranin A-immunoreactive neuroendocrine cells, of which the main cell type was the histidine decarboxylase-immunoreactive enterochromaffin-like (ECL) cell. The association of clusterin with neuroendocrine differentiation was further confirmed in human gastric ECL carcinoids. Interestingly, in hypergastrinemic rats, clusterin-immunoreactive cells formed distinct groups of diverse cells at the base of many glands. Our results suggest that clusterin may contribute to gastrin's growth-promoting effect on the oxyntic mucosa.
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Affiliation(s)
- Christina Sæten Fjeldbo
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
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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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Rantala JK, Mäkelä R, Aaltola AR, Laasola P, Mpindi JP, Nees M, Saviranta P, Kallioniemi O. A cell spot microarray method for production of high density siRNA transfection microarrays. BMC Genomics 2011; 12:162. [PMID: 21443765 PMCID: PMC3073923 DOI: 10.1186/1471-2164-12-162] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2010] [Accepted: 03/28/2011] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND High-throughput RNAi screening is widely applied in biological research, but remains expensive, infrastructure-intensive and conversion of many assays to HTS applications in microplate format is not feasible. RESULTS Here, we describe the optimization of a miniaturized cell spot microarray (CSMA) method, which facilitates utilization of the transfection microarray technique for disparate RNAi analyses. To promote rapid adaptation of the method, the concept has been tested with a panel of 92 adherent cell types, including primary human cells. We demonstrate the method in the systematic screening of 492 GPCR coding genes for impact on growth and survival of cultured human prostate cancer cells. CONCLUSIONS The CSMA method facilitates reproducible preparation of highly parallel cell microarrays for large-scale gene knockdown analyses. This will be critical towards expanding the cell based functional genetic screens to include more RNAi constructs, allow combinatorial RNAi analyses, multi-parametric phenotypic readouts or comparative analysis of many different cell types.
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Affiliation(s)
- Juha K Rantala
- Medical Biotechnology, VTT Technical Research Centre of Finland, 20521 Turku, Finland.
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Tuzmen S, Tuzmen P, Arora S, Mousses S, Azorsa D. RNAi-based functional pharmacogenomics. Methods Mol Biol 2011; 700:271-90. [PMID: 21204040 DOI: 10.1007/978-1-61737-954-3_18] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Experimental alteration of gene expression is a powerful technique for functional characterization of disease genes. RNA interference (RNAi) is a naturally occurring mechanism of gene regulation, which is triggered by the introduction of double-stranded RNA into a cell. This phenomenon can be synthetically exploited to down-regulate expression of specific genes by transfecting mammalian cells with synthetic short interfering RNAs (siRNAs). These siRNAs can be designed to silence the expression of specific genes bearing a particular target sequence in high-throughput (HT) siRNA experimental systems and may potentially be presented as a therapeutic strategy for inhibiting transcriptional regulation of genes. This can constitute a strategy that can inhibit targets that are not tractable by small molecules such as chemical compounds. Large-scale experiments using low-dose drug exposure combined with siRNA also represent a promising discovery strategy for the purpose of identifying synergistic targets that facilitate synthetic lethal combination phenotypes. In light of such advantageous applications, siRNA technology has become an ideal research tool for studying gene function. In this chapter, we focus on the application of RNAi, with particular focus on HT siRNA phenotype profiling, to support cellular pharmacogenomics.
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Affiliation(s)
- Sukru Tuzmen
- Pharmaceutical Genomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA.
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Functional studies on RNA-transfected cell microarrays. Methods Mol Biol 2010; 629:175-91. [PMID: 20387150 DOI: 10.1007/978-1-60761-657-3_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
RNA-transfected cell microarray shows great promise in functional genomics. By printing siRNA complexed with transfection reagent on glass slides, arrays of transfected cells are formed in which the phenotypic consequences of gene suppression can be investigated. Using reporter plasmids with fluorescence intensity as output data, we have developed a strategy for statistical analysis of the intensity data from medium-scale functional studies using data from several experimental replicates.
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