1
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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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2
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Adams FF, Hoffmann T, Zuber J, Heckl D, Schambach A, Schwarzer A. Pooled Generation of Lentiviral Tetracycline-Regulated microRNA Embedded Short Hairpin RNA Libraries. Hum Gene Ther Methods 2018; 29:16-29. [PMID: 29325442 DOI: 10.1089/hgtb.2017.182] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Short hairpin RNA (shRNA) screens are powerful tools to probe genetic dependencies in loss-of-function studies, such as the identification of therapeutic targets in cancer research. Lentivirally delivered shRNAs embedded in endogenous microRNA contexts (shRNAmiRs) mediate efficient long-term suppression of target genes suitable for numerous experimental contexts and clinical applications. Here, an easy-to-use laboratory protocol is described, covering the design and pooled assembly of focused shRNAmiR libraries into an optimized, Tet-inducible all-in-one lentiviral vector, packaging of viral particles, followed by retrieval and quantification of hairpin sequences after cellular DNA-recovery. Starting from a gene list to the identification of hits, the protocol enables shRNA screens within 6 weeks.
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Affiliation(s)
- Felix F Adams
- 1 Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
| | - Thomas Hoffmann
- 2 Research Institute of Molecular Pathology (IMP), Vienna, Austria
| | - Johannes Zuber
- 2 Research Institute of Molecular Pathology (IMP), Vienna, Austria
| | - Dirk Heckl
- 3 Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Axel Schambach
- 1 Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany .,4 Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Adrian Schwarzer
- 1 Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany .,5 Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
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3
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Azorsa DO, Turnidge MA, Arora S. Data Analysis for High-Throughput RNAi Screening. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2016; 1470:247-60. [PMID: 27581298 DOI: 10.1007/978-1-4939-6337-9_19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
High-throughput RNA interference (HT-RNAi) screening is an effective technology to help identify important genes and pathways involved in a biological process. Analysis of high-throughput RNAi screening data is a critical part of this technology, and many analysis methods have been described. Here, we summarize the workflow and types of analyses commonly used in high-throughput RNAi screening.
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Affiliation(s)
- David O Azorsa
- Institute of Molecular Medicine, Phoenix Children's Hospital, Phoenix, AZ, USA. .,Department of Child Health, University of Arizona College of Medicine - Phoenix, Phoenix, AZ, USA.
| | - Megan A Turnidge
- Department of Child Health, University of Arizona College of Medicine - Phoenix, Phoenix, AZ, USA.,School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Shilpi Arora
- Constellation Pharmaceuticals, Cambridge, MA, USA
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4
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Mattiazzi Usaj M, Styles EB, Verster AJ, Friesen H, Boone C, Andrews BJ. High-Content Screening for Quantitative Cell Biology. Trends Cell Biol 2016; 26:598-611. [PMID: 27118708 DOI: 10.1016/j.tcb.2016.03.008] [Citation(s) in RCA: 161] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 03/21/2016] [Accepted: 03/22/2016] [Indexed: 12/25/2022]
Abstract
High-content screening (HCS), which combines automated fluorescence microscopy with quantitative image analysis, allows the acquisition of unbiased multiparametric data at the single cell level. This approach has been used to address diverse biological questions and identify a plethora of quantitative phenotypes of varying complexity in numerous different model systems. Here, we describe some recent applications of HCS, ranging from the identification of genes required for specific biological processes to the characterization of genetic interactions. We review the steps involved in the design of useful biological assays and automated image analysis, and describe major challenges associated with each. Additionally, we highlight emerging technologies and future challenges, and discuss how the field of HCS might be enhanced in the future.
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Affiliation(s)
| | - Erin B Styles
- The Donnelly Centre, University of Toronto, Toronto, ON M5S3E1, Canada
| | - Adrian J Verster
- The Donnelly Centre, University of Toronto, Toronto, ON M5S3E1, Canada
| | - Helena Friesen
- The Donnelly Centre, University of Toronto, Toronto, ON M5S3E1, Canada
| | - Charles Boone
- The Donnelly Centre, University of Toronto, Toronto, ON M5S3E1, Canada
| | - Brenda J Andrews
- The Donnelly Centre, University of Toronto, Toronto, ON M5S3E1, Canada.
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5
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Di Rocco G, Verdina A, Gatti V, Virdia I, Toietta G, Todaro M, Stassi G, Soddu S. Apoptosis induced by a HIPK2 full-length-specific siRNA is due to off-target effects rather than prevalence of HIPK2-Δe8 isoform. Oncotarget 2016; 7:1675-86. [PMID: 26625198 PMCID: PMC4811489 DOI: 10.18632/oncotarget.6423] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 11/15/2015] [Indexed: 01/05/2023] Open
Abstract
Small interfering RNAs (siRNAs) are widely used to study gene function and extensively exploited for their potential therapeutic applications. HIPK2 is an evolutionary conserved kinase that binds and phosphorylates several proteins directly or indirectly related to apoptosis. Recently, an alternatively spliced isoform skipping 81 nucleotides of exon 8 (Hipk2-Δe8) has been described. Selective depletion of Hipk2 full-length (Hipk2-FL) with a specific siRNA that spares the Hipk2-Δe8 isoform has been shown to strongly induce apoptosis, suggesting an unpredicted dominant-negative effect of Hipk2-FL over the Δe8 isoform. From this observation, we sought to take advantage and assessed the therapeutic potential of generating Hipk2 isoform unbalance in tumor-initiating cells derived from colorectal cancer patients. Strong reduction of cell viability was induced in vitro and in vivo by the originally described exon 8-specific siRNA, supporting a potential therapeutic application. However, validation analyses performed with additional exon8-specific siRNAs with different stabilities showed that all exon8-targeting siRNAs can induce comparable Hipk2 isoform unbalance but only the originally reported e8-siRNA promotes cell death. These data show that loss of viability does not depend on the prevalence of Hipk2-Δe8 isoform but it is rather due to microRNA-like off-target effects.
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Affiliation(s)
- Giuliana Di Rocco
- Department of Research, Advanced Diagnostics, and Technological Innovation, Regina Elena National Cancer Institute, Rome, Italy
| | - Alessandra Verdina
- Department of Research, Advanced Diagnostics, and Technological Innovation, Regina Elena National Cancer Institute, Rome, Italy
| | - Veronica Gatti
- Department of Research, Advanced Diagnostics, and Technological Innovation, Regina Elena National Cancer Institute, Rome, Italy
| | - Ilaria Virdia
- Department of Research, Advanced Diagnostics, and Technological Innovation, Regina Elena National Cancer Institute, Rome, Italy
| | - Gabriele Toietta
- Department of Research, Advanced Diagnostics, and Technological Innovation, Regina Elena National Cancer Institute, Rome, Italy
| | - Matilde Todaro
- Department of Surgical and Oncological Sciences, Cellular and Molecular Pathophysiology Laboratory, University of Palermo, Palermo, Italy
| | - Giorgio Stassi
- Department of Surgical and Oncological Sciences, Cellular and Molecular Pathophysiology Laboratory, University of Palermo, Palermo, Italy
| | - Silvia Soddu
- Department of Research, Advanced Diagnostics, and Technological Innovation, Regina Elena National Cancer Institute, Rome, Italy
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6
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Lee J, Galloway R, Grandjean G, Jacob J, Humphries J, Bartholomeusz C, Goodstal S, Lim B, Bartholomeusz G, Ueno NT, Rao A. Comprehensive Two- and Three-Dimensional RNAi Screening Identifies PI3K Inhibition as a Complement to MEK Inhibitor AS703026 for Combination Treatment of Triple-Negative Breast Cancer. J Cancer 2015; 6:1306-19. [PMID: 26640591 PMCID: PMC4643087 DOI: 10.7150/jca.13266] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 08/08/2015] [Indexed: 12/12/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is a major cause of death among breast cancer patients that results from intrinsic and acquired resistance to systemic chemotherapies. To identify novel targets for effective treatment of TNBC through combination strategies with MEK inhibitor (AS703026), we used a novel method of combining high-throughput two- and three-dimensional (2D and 3D) RNAi screening. TNBC cells were transfected with a kinome siRNA library comprising siRNA targeting 790 kinases under both 2D and 3D culture conditions with or without AS703026. Molecule activity predictor analysis revealed the PI3K pathway as the major target pathway in our RNAi combination studies in TNBC. We found that PI3K inhibitor SAR245409 (also called XL765) combined with AS703026 synergistically inhibited proliferation compared with either drug alone (P < 0.001). Reduced in vitro colony formation (P < 0.001) and migration and invasion ability were also observed with the combination treatment (P<0.01). Our data suggest that SAR245409 combined with AS703026 may be effective in patients with TNBC. We conclude that a novel powerful high-throughput RNAi assays were able to identify anti-cancer drugs as single or combinational agents. Integrated and multi-system RNAi screening methods can complement difference between in vitro and in vivo culture conditions, and enriches targets that are close to the in vivo condition.
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Affiliation(s)
- Jangsoon Lee
- 1. Section of Translational Breast Cancer Research and Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, Department of Breast Medical Oncology - Unit 1354, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA
| | - Rachael Galloway
- 2. Department of Bioinformatics and Computational Biology - Unit 1410, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA
| | - Geoff Grandjean
- 3. Department of Experimental Therapeutics - Unit 1950, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA
| | - Justin Jacob
- 3. Department of Experimental Therapeutics - Unit 1950, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA
| | - Juliane Humphries
- 1. Section of Translational Breast Cancer Research and Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, Department of Breast Medical Oncology - Unit 1354, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA
| | - Chandra Bartholomeusz
- 1. Section of Translational Breast Cancer Research and Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, Department of Breast Medical Oncology - Unit 1354, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA
| | - Samantha Goodstal
- 4. EMD Serono Research & Development Institute, Inc., 45A Middlesex Turnpike, Billerica, MA, 01821, USA
| | - Bora Lim
- 1. Section of Translational Breast Cancer Research and Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, Department of Breast Medical Oncology - Unit 1354, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA
| | - Geoffrey Bartholomeusz
- 3. Department of Experimental Therapeutics - Unit 1950, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA
| | - Naoto T Ueno
- 1. Section of Translational Breast Cancer Research and Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, Department of Breast Medical Oncology - Unit 1354, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA
| | - Arvind Rao
- 2. Department of Bioinformatics and Computational Biology - Unit 1410, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA
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7
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Φ-score: A cell-to-cell phenotypic scoring method for sensitive and selective hit discovery in cell-based assays. Sci Rep 2015; 5:14221. [PMID: 26382112 PMCID: PMC4585642 DOI: 10.1038/srep14221] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 08/07/2015] [Indexed: 11/25/2022] Open
Abstract
Phenotypic screening monitors phenotypic changes induced by perturbations, including those generated by drugs or RNA interference. Currently-used methods for scoring screen hits have proven to be problematic, particularly when applied to physiologically relevant conditions such as low cell numbers or inefficient transfection. Here, we describe the Φ-score, which is a novel scoring method for the identification of phenotypic modifiers or hits in cell-based screens. Φ-score performance was assessed with simulations, a validation experiment and its application to gene identification in a large-scale RNAi screen. Using robust statistics and a variance model, we demonstrated that the Φ-score showed better sensitivity, selectivity and reproducibility compared to classical approaches. The improved performance of the Φ-score paves the way for cell-based screening of primary cells, which are often difficult to obtain from patients in sufficient numbers. We also describe a dedicated merging procedure to pool scores from small interfering RNAs targeting the same gene so as to provide improved visualization and hit selection.
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8
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Abstract
Deciphering the many interactions that occur between a virus and host cell over the course of infection is paramount to understanding mechanisms of pathogenesis and to the future development of antiviral therapies. Over the past decade, researchers have started to understand these complicated relationships through the development of methodologies, including advances in RNA interference, proteomics, and the development of genetic tools such as haploid cell lines, allowing high-throughput screening to identify critical contact points between virus and host. These advances have produced a wealth of data regarding host factors hijacked by viruses to promote infection, as well as antiviral factors responsible for subverting viral infection. This review highlights findings from virus-host screens and discusses our thoughts on the direction of screening strategies moving forward.
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Affiliation(s)
- Holly Ramage
- Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104; ,
| | - Sara Cherry
- Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104; ,
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9
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Lietard J, Hassler MR, Fakhoury J, Damha MJ. An orthogonal photolabile linker for the complete "on-support" synthesis/fast deprotection/hybridization of RNA. Chem Commun (Camb) 2015; 50:15063-6. [PMID: 25329642 DOI: 10.1039/c4cc07153k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The preparation of a polystyrene solid support decorated with a photolabile linker is described. The entire post-synthetic processing of RNA can be carried out in the solid phase in a minimum amount of time. The deprotected RNA is available for "on-support" hybridization and photolysis releases siRNA duplexes under mild, neutral conditions.
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Affiliation(s)
- Jory Lietard
- Department of Chemistry, McGill University, Montréal, Québec H3A 0B8, Canada.
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10
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Zhang N, Park YD, Williamson PR. New technology and resources for cryptococcal research. Fungal Genet Biol 2015; 78:99-107. [PMID: 25460849 PMCID: PMC4433448 DOI: 10.1016/j.fgb.2014.11.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Revised: 11/02/2014] [Accepted: 11/06/2014] [Indexed: 11/26/2022]
Abstract
Rapid advances in molecular biology and genome sequencing have enabled the generation of new technology and resources for cryptococcal research. RNAi-mediated specific gene knock down has become routine and more efficient by utilizing modified shRNA plasmids and convergent promoter RNAi constructs. This system was recently applied in a high-throughput screen to identify genes involved in host-pathogen interactions. Gene deletion efficiencies have also been improved by increasing rates of homologous recombination through a number of approaches, including a combination of double-joint PCR with split-marker transformation, the use of dominant selectable markers and the introduction of Cre-Loxp systems into Cryptococcus. Moreover, visualization of cryptococcal proteins has become more facile using fusions with codon-optimized fluorescent tags, such as green or red fluorescent proteins or, mCherry. Using recent genome-wide analytical tools, new transcriptional factors and regulatory proteins have been identified in novel virulence-related signaling pathways by employing microarray analysis, RNA-sequencing and proteomic analysis.
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Affiliation(s)
- Nannan Zhang
- Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institution of Health, Bethesda, MD, United States
| | - Yoon-Dong Park
- Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institution of Health, Bethesda, MD, United States
| | - Peter R Williamson
- Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institution of Health, Bethesda, MD, United States.
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11
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Finkbeiner S, Frumkin M, Kassner PD. Cell-based screening: extracting meaning from complex data. Neuron 2015; 86:160-74. [PMID: 25856492 PMCID: PMC4457442 DOI: 10.1016/j.neuron.2015.02.023] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 09/23/2014] [Accepted: 01/22/2015] [Indexed: 01/23/2023]
Abstract
Unbiased discovery approaches have the potential to uncover neurobiological insights into CNS disease and lead to the development of therapies. Here, we review lessons learned from imaging-based screening approaches and recent advances in these areas, including powerful new computational tools to synthesize complex data into more useful knowledge that can reliably guide future research and development.
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Affiliation(s)
- Steven Finkbeiner
- Director of the Taube/Koret Center for Neurodegenerative Disease and the Hellman Family Foundation Program in Alzheimer's Disease Research, Gladstone Institute of Neurological Disease, San Francisco, CA 94158, USA; Departments of Neurology and Physiology, University of California, San Francisco, San Francisco, CA 94143, USA.
| | - Michael Frumkin
- Director of Engineering, Research, Google, Inc., 1600 Amphitheatre Parkway, Mountain View, CA 94043, USA
| | - Paul D Kassner
- Director of Research, Amgen, Inc., 1120 Veterans Boulevard South, San Francisco, CA 94080, USA
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12
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Abstract
RNAi screening has gained popularity in recent years, due to its usefulness in systematic investigations of biological pathways. Combined with high-content screening and advances in imaging and analysis methods, it can enable detailed genetic characterization of cellular processes such as protein glycosylation, a major function of the Golgi apparatus. Glycosylation concerns about one third of all human proteins and regulates various cellular behaviors. Yet the methods available to study it are limited and not easily accessible. In this chapter, we detail a step-by-step method to systematically and quantitatively investigate glycosylation using fluorescent lectin staining, following high-throughput RNAi-based downregulation of gene activities. We also provide a workflow for downstream analysis of the data generated.
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Affiliation(s)
- Germaine Y Goh
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore
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13
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O’Connor JE, Herrera G, Martínez-Romero A, de Oyanguren FS, Díaz L, Gomes A, Balaguer S, Callaghan RC. Systems Biology and immune aging. Immunol Lett 2014; 162:334-45. [DOI: 10.1016/j.imlet.2014.09.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2014] [Accepted: 09/12/2014] [Indexed: 10/24/2022]
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14
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Chang TY, Shi P, Steinmeyer JD, Chatnuntawech I, Tillberg P, Love KT, Eimon PM, Anderson DG, Yanik MF. Organ-targeted high-throughput in vivo biologics screen identifies materials for RNA delivery. Integr Biol (Camb) 2014; 6:926-34. [PMID: 25184623 PMCID: PMC4350364 DOI: 10.1039/c4ib00150h] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Therapies based on biologics involving delivery of proteins, DNA, and RNA are currently among the most promising approaches. However, although large combinatorial libraries of biologics and delivery vehicles can be readily synthesized, there are currently no means to rapidly characterize them in vivo using animal models. Here, we demonstrate high-throughput in vivo screening of biologics and delivery vehicles by automated delivery into target tissues of small vertebrates with developed organs. Individual zebrafish larvae are automatically oriented and immobilized within hydrogel droplets in an array format using a microfluidic system, and delivery vehicles are automatically microinjected to target organs with high repeatability and precision. We screened a library of lipid-like delivery vehicles for their ability to facilitate the expression of protein-encoding RNAs in the central nervous system. We discovered delivery vehicles that are effective in both larval zebrafish and rats. Our results showed that the in vivo zebrafish model can be significantly more predictive of both false positives and false negatives in mammals than in vitro mammalian cell culture assays. Our screening results also suggest certain structure-activity relationships, which can potentially be applied to design novel delivery vehicles.
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Affiliation(s)
- Tsung-Yao Chang
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Peng Shi
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Mechanical and Biomedical Engineering, City University of Hong Kong, Hong Kong, China
| | - Joseph D. Steinmeyer
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Itthi Chatnuntawech
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Paul Tillberg
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Kevin T. Love
- Department of Chemical Engineering, Institute of Medical Engineering and Science, Division of Health Science and Technology, David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Peter M. Eimon
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Daniel G. Anderson
- Department of Chemical Engineering, Institute of Medical Engineering and Science, Division of Health Science and Technology, David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Mehmet Fatih Yanik
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- ETH, Zurich, Switzerland
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15
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O'Connor JE, Herrera G, Martínez-Romero A, Oyanguren FSD, Díaz L, Gomes A, Balaguer S, Callaghan RC. WITHDRAWN: Systems Biology and Immune Aging. Immunol Lett 2014:S0165-2478(14)00197-7. [PMID: 25251659 DOI: 10.1016/j.imlet.2014.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 09/12/2014] [Indexed: 10/24/2022]
Abstract
The Publisher regrets that this article is an accidental duplication of anarticle that has already been published, http://dx.doi.org/10.1016/j.imlet.2014.09.009. The duplicate article has therefore been withdrawn.
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Affiliation(s)
- José-Enrique O'Connor
- Laboratory of Translational Cytomics, Joint Research Unit, The University of Valencia and Principe Felipe Research Center, Valencia, Spain; Cytometry Laboratory, Incliva Foundation, Clinical University Hospital, The University of Valencia, Valencia, Spain.
| | - Guadalupe Herrera
- Laboratory of Translational Cytomics, Joint Research Unit, The University of Valencia and Principe Felipe Research Center, Valencia, Spain; Cytometry Laboratory, Incliva Foundation, Clinical University Hospital, The University of Valencia, Valencia, Spain
| | - Alicia Martínez-Romero
- Cytometry Technological Service, Principe Felipe Research Center, Valencia, Spain; Cytometry Laboratory, Incliva Foundation, Clinical University Hospital, The University of Valencia, Valencia, Spain
| | - Francisco Sala-de Oyanguren
- Laboratory of Translational Cytomics, Joint Research Unit, The University of Valencia and Principe Felipe Research Center, Valencia, Spain; Cytometry Laboratory, Incliva Foundation, Clinical University Hospital, The University of Valencia, Valencia, Spain
| | - Laura Díaz
- Laboratory of Translational Cytomics, Joint Research Unit, The University of Valencia and Principe Felipe Research Center, Valencia, Spain; Cytometry Laboratory, Incliva Foundation, Clinical University Hospital, The University of Valencia, Valencia, Spain
| | - Angela Gomes
- Laboratory of Translational Cytomics, Joint Research Unit, The University of Valencia and Principe Felipe Research Center, Valencia, Spain; Cytometry Laboratory, Incliva Foundation, Clinical University Hospital, The University of Valencia, Valencia, Spain
| | - Susana Balaguer
- Laboratory of Translational Cytomics, Joint Research Unit, The University of Valencia and Principe Felipe Research Center, Valencia, Spain; Cytometry Laboratory, Incliva Foundation, Clinical University Hospital, The University of Valencia, Valencia, Spain
| | - Robert C Callaghan
- Department of Pathology, Faculty of Medicine, The University of Valencia, Valencia, Spain; Cytometry Laboratory, Incliva Foundation, Clinical University Hospital, The University of Valencia, Valencia, Spain
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16
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Liberali P, Snijder B, Pelkmans L. A Hierarchical Map of Regulatory Genetic Interactions in Membrane Trafficking. Cell 2014; 157:1473-1487. [DOI: 10.1016/j.cell.2014.04.029] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Revised: 01/30/2014] [Accepted: 04/10/2014] [Indexed: 11/29/2022]
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17
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Neyen C, Bretscher AJ, Binggeli O, Lemaitre B. Methods to study Drosophila immunity. Methods 2014; 68:116-28. [PMID: 24631888 DOI: 10.1016/j.ymeth.2014.02.023] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Revised: 02/15/2014] [Accepted: 02/18/2014] [Indexed: 01/23/2023] Open
Abstract
Innate immune mechanisms are well conserved throughout evolution, and many theoretical concepts, molecular pathways and gene networks are applicable to invertebrate model organisms as much as vertebrate ones. Drosophila immunity research benefits from an easily manipulated genome, a fantastic international resource of transgenic tools and over a quarter century of accumulated techniques and approaches to study innate immunity. Here we present a short collection of ways to challenge the fruit fly immune system with various pathogens and parasites, as well as read-outs to assess its functions, including cellular and humoral immune responses. Our review covers techniques for assessing the kinetics and efficiency of immune responses quantitatively and qualitatively, such as survival analysis, bacterial persistence, antimicrobial peptide gene expression, phagocytosis and melanisation assays. Finally, we offer a toolkit of Drosophila strains available to the research community for current and future research.
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Affiliation(s)
- Claudine Neyen
- Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 19, 1015 Lausanne, Switzerland.
| | - Andrew J Bretscher
- Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 19, 1015 Lausanne, Switzerland
| | - Olivier Binggeli
- Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 19, 1015 Lausanne, Switzerland
| | - Bruno Lemaitre
- Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 19, 1015 Lausanne, Switzerland.
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18
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Mohr SE. RNAi screening in Drosophila cells and in vivo. Methods 2014; 68:82-8. [PMID: 24576618 DOI: 10.1016/j.ymeth.2014.02.018] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 02/07/2014] [Accepted: 02/13/2014] [Indexed: 12/31/2022] Open
Abstract
Here, I discuss how RNAi screening can be used effectively to uncover gene function. Specifically, I discuss the types of high-throughput assays that can be done in Drosophila cells and in vivo, RNAi reagent design and available reagent collections, automated screen pipelines, analysis of screen results, and approaches to RNAi results verification.
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Affiliation(s)
- Stephanie E Mohr
- Drosophila RNAi Screening Center, Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, United States.
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19
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Böhmer FD, Friedrich K. Protein tyrosine phosphatases as wardens of STAT signaling. JAKSTAT 2014; 3:e28087. [PMID: 24778927 DOI: 10.4161/jkst.28087] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 02/03/2014] [Accepted: 02/03/2014] [Indexed: 02/07/2023] Open
Abstract
Signaling by signal transducers and activators of transcription (STATs) is controlled at many levels of the signaling cascade. Protein tyrosine phosphatases (PTPs) regulate STAT activation at several layers, including direct pSTAT dephosphorylation in both cytoplasm and nucleus. Despite the importance of this regulation mode, many aspects are still incompletely understood, e.g., the identity of PTPs acting on certain members of the STAT family. After a brief introduction into the STAT and PTP families, we discuss here the current knowledge on PTP mediated regulation of STAT activity, focusing on the interaction of individual STATs with specific PTPs. Finally, we highlight open questions and propose important tasks of future research.
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Affiliation(s)
- Frank-D Böhmer
- Institute of Molecular Cell Biology; CMB; Jena University Hospital; Jena, Germany
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20
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Karimi N, Samavi S, Shirani S. Lossless compression of RNAi fluorescence images using regional fluctuations of pixels. IEEE J Biomed Health Inform 2013; 17:259-68. [PMID: 24235106 DOI: 10.1109/jbhi.2012.2235453] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
RNA interference (RNAi) is considered one of the most powerful genomic tools which allows the study of drug discovery and understanding of the complex cellular processes by high-content screens. This field of study, which was the subject of 2006 Nobel Prize of medicine, has drastically changed the conventional methods of analysis of genes. A large number of images have been produced by the RNAi experiments. Even though a number of capable special purpose methods have been proposed recently for the processing of RNAi images but there is no customized compression scheme for these images. Hence, highly proficient tools are required to compress these images. In this paper, we propose a new efficient lossless compression scheme for the RNAi images. A new predictor specifically designed for these images is proposed. It is shown that pixels can be classified into three categories based on their intensity distributions. Using classification of pixels based on the intensity fluctuations among the neighbors of a pixel a context-based method is designed. Comparisons of the proposed method with the existing state-of-the-art lossless compression standards and well-known general-purpose methods are performed to show the efficiency of the proposed method.
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21
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Madhunapantula SV, Sharma A, Gowda R, Robertson GP. Identification of glycogen synthase kinase 3α as a therapeutic target in melanoma. Pigment Cell Melanoma Res 2013; 26:886-99. [PMID: 24034838 DOI: 10.1111/pcmr.12156] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 08/05/2013] [Indexed: 12/14/2022]
Abstract
Deregulated expression or activity of kinases can lead to melanomas, but often the particular kinase isoform causing the effect is not well established, making identification and validation of different isoforms regulating disease development especially important. To accomplish this objective, an siRNA screen was undertaken that which identified glycogen synthase kinase 3α (GSK3α) as an important melanoma growth regulator. Melanocytes and melanoma cell lines representing various stages of melanoma tumor progression expressed both GSK3α and GSK3β, but analysis of tumors in patients with melanoma showed elevated expression of GSK3α in 72% of samples, which was not observed for GSK3β. Furthermore, 80% of tumors in patients with melanoma expressed elevated levels of catalytically active phosphorylated GSK3α (pGSK3αY279), but not phosphorylated GSK3β (pGSK3βY216). siRNA-mediated reduction in GSK3α protein levels reduced melanoma cell survival and proliferation, sensitized cells to apoptosis-inducing agents and decreased xenografted tumor development by up to 56%. Mechanistically, inhibiting GSK3α expression using siRNA or the pharmacological agent AR-A014418 arrested melanoma cells in the G0/G1 phase of the cell cycle and induced apoptotic death to retard tumorigenesis. Therefore, GSK3α is a key therapeutic target in melanoma.
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Affiliation(s)
- SubbaRao V Madhunapantula
- Department of Pharmacology, The Pennsylvania State University College of Medicine, Hershey, PA, USA; Penn State Melanoma Center, The Pennsylvania State University College of Medicine, Hershey, PA, USA; Penn State Melanoma Therapeutics Program, The Pennsylvania State University College of Medicine, Hershey, PA, USA
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22
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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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23
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Ambjørn M, Dubreuil V, Miozzo F, Nigon F, Møller B, Issazadeh-Navikas S, Berg J, Lees M, Sap J. A loss-of-function screen for phosphatases that regulate neurite outgrowth identifies PTPN12 as a negative regulator of TrkB tyrosine phosphorylation. PLoS One 2013; 8:e65371. [PMID: 23785422 PMCID: PMC3681791 DOI: 10.1371/journal.pone.0065371] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Accepted: 04/30/2013] [Indexed: 11/28/2022] Open
Abstract
Alterations in function of the neurotrophin BDNF are associated with neurodegeneration, cognitive decline, and psychiatric disorders. BDNF promotes axonal outgrowth and branching, regulates dendritic tree morphology and is important for axonal regeneration after injury, responses that largely result from activation of its tyrosine kinase receptor TrkB. Although intracellular neurotrophin (NT) signaling presumably reflects the combined action of kinases and phosphatases, little is known about the contributions of the latter to TrkB regulation. The issue is complicated by the fact that phosphatases belong to multiple independently evolved families, which are rarely studied together. We undertook a loss-of-function RNA-interference-based screen of virtually all known (254) human phosphatases to understand their function in BDNF/TrkB-mediated neurite outgrowth in differentiated SH-SY5Y cells. This approach identified phosphatases from diverse families, which either positively or negatively modulate BDNF-TrkB-mediated neurite outgrowth, and most of which have little or no previously established function related to NT signaling. “Classical” protein tyrosine phosphatases (PTPs) accounted for 13% of the candidate regulatory phosphatases. The top classical PTP identified as a negative regulator of BDNF-TrkB-mediated neurite outgrowth was PTPN12 (also called PTP-PEST). Validation and follow-up studies showed that endogenous PTPN12 antagonizes tyrosine phosphorylation of TrkB itself, and the downstream activation of ERK1/2. We also found PTPN12 to negatively regulate phosphorylation of p130cas and FAK, proteins with previously described functions related to cell motility and growth cone behavior. Our data provide the first comprehensive survey of phosphatase function in NT signaling and neurite outgrowth. They reveal the complexity of phosphatase control, with several evolutionarily unrelated phosphatase families cooperating to affect this biological response, and hence the relevance of considering all phosphatase families when mining for potentially druggable targets.
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Affiliation(s)
- Malene Ambjørn
- Department of Biomedical Sciences and Biotechnology Research and Innovation Centre (BRIC), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Véronique Dubreuil
- Epigenetics and Cell Fate, University of Paris, Sorbonne Paris Cité, Paris, France
| | - Federico Miozzo
- Epigenetics and Cell Fate, University of Paris, Sorbonne Paris Cité, Paris, France
| | - Fabienne Nigon
- Epigenetics and Cell Fate, University of Paris, Sorbonne Paris Cité, Paris, France
| | - Bente Møller
- Department of Biomedical Sciences and Biotechnology Research and Innovation Centre (BRIC), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Shohreh Issazadeh-Navikas
- Department of Biomedical Sciences and Biotechnology Research and Innovation Centre (BRIC), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jacob Berg
- Department of Wind Energy, Technical University of Denmark, Roskilde, Denmark
| | - Michael Lees
- Department of Biomedical Sciences and Biotechnology Research and Innovation Centre (BRIC), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jan Sap
- Department of Biomedical Sciences and Biotechnology Research and Innovation Centre (BRIC), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Epigenetics and Cell Fate, University of Paris, Sorbonne Paris Cité, Paris, France
- * E-mail:
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24
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Abstract
Gene silencing by RNA interference (RNAi) has become a standard method for the characterization of gene function in mammalian cells. Short hairpin (sh) RNAs expressed from stably integrated vectors mediate gene knockdown both in cultured cells and in mice, presenting a fast alternative to gene knockout approaches. We describe three strategies to control gene silencing in mice that can be applied to any transcript of interest. This shRNA based approach enables either i) constitutive body-wide knockdown, ii) cell type-specific knockdown controlled by Cre recombinase, or iii) inducible body-wide knockdown controlled by doxycycline. For reliable expression the shRNA vector of interest is inserted into a Rosa26 docking site of ES cells by a site-specific recombinase. These ES cells can then be used to generate shRNA transgenic mice. This technology enables the production of adult knockdown mice within 11 months for an expedite in vivo validation of drug targets.
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25
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Morita E, Arii J, Christensen D, Votteler J, Sundquist WI. Attenuated protein expression vectors for use in siRNA rescue experiments. Biotechniques 2012; 0:1-5. [PMID: 22877307 PMCID: PMC3759224 DOI: 10.2144/000113909] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Accepted: 07/13/2012] [Indexed: 11/23/2022] Open
Abstract
Transient transfection of small interfering RNA (siRNA) provides a powerful approach for studying cellular protein functions, particularly when the target protein can be re-expressed from an exogenous siRNA-resistant construct in order to rescue the knockdown phenotype, confirm siRNA target specificity, and support mutational analyses. Rescue experiments often fail, however, when siRNA-resistant constructs are expressed at suboptimal levels. Here, we describe an ensemble of mammalian protein expression vectors with CMV promoters of differing strengths. Using CHMP2A rescue of HIV-1 budding, we show that these vectors can combine high-transfection efficiencies with tunable protein expression levels to optimize the rescue of cellular phenotypes induced by siRNA transfection.
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Affiliation(s)
- Eiji Morita
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
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26
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Erdmann G, Volz C, Boutros M. Systematic approaches to dissect biological processes in stem cells by image-based screening. Biotechnol J 2012; 7:768-78. [DOI: 10.1002/biot.201200117] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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27
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Discovery of small molecule cancer drugs: successes, challenges and opportunities. Mol Oncol 2012; 6:155-76. [PMID: 22440008 PMCID: PMC3476506 DOI: 10.1016/j.molonc.2012.02.004] [Citation(s) in RCA: 374] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Accepted: 02/20/2012] [Indexed: 02/07/2023] Open
Abstract
The discovery and development of small molecule cancer drugs has been revolutionised over the last decade. Most notably, we have moved from a one-size-fits-all approach that emphasized cytotoxic chemotherapy to a personalised medicine strategy that focuses on the discovery and development of molecularly targeted drugs that exploit the particular genetic addictions, dependencies and vulnerabilities of cancer cells. These exploitable characteristics are increasingly being revealed by our expanding understanding of the abnormal biology and genetics of cancer cells, accelerated by cancer genome sequencing and other high-throughput genome-wide campaigns, including functional screens using RNA interference. In this review we provide an overview of contemporary approaches to the discovery of small molecule cancer drugs, highlighting successes, current challenges and future opportunities. We focus in particular on four key steps: Target validation and selection; chemical hit and lead generation; lead optimization to identify a clinical drug candidate; and finally hypothesis-driven, biomarker-led clinical trials. Although all of these steps are critical, we view target validation and selection and the conduct of biology-directed clinical trials as especially important areas upon which to focus to speed progress from gene to drug and to reduce the unacceptably high attrition rate during clinical development. Other challenges include expanding the envelope of druggability for less tractable targets, understanding and overcoming drug resistance, and designing intelligent and effective drug combinations. We discuss not only scientific and technical challenges, but also the assessment and mitigation of risks as well as organizational, cultural and funding problems for cancer drug discovery and development, together with solutions to overcome the 'Valley of Death' between basic research and approved medicines. We envisage a future in which addressing these challenges will enhance our rapid progress towards truly personalised medicine for cancer patients.
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28
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Abstract
The discovery of RNA interference (RNAi) and the development of technologies exploiting its biology have enabled scientists to rapidly examine the consequences of depleting a particular gene product in a cell or an animal. The availability of genome-wide RNAi libraries targeting the mouse and human genomes has made it possible to carry out large scale, phenotype-based screens, which have yielded seminal information on diverse cellular processes ranging from virology to cancer biology. Today, several strategies are available to perform RNAi screens, each with their own technical and monetary considerations. Special care and budgeting must be taken into account during the design of these screens in order to obtain reliable results. In this review, we discuss a number of critical aspects to consider when planning an effective RNAi screening strategy, including selecting the right biological system, designing an appropriate selection scheme, optimizing technical aspects of the screen, and validating and verifying the hits. Similar to an artistic production, what happens behind the screen has a direct impact on its success.
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Affiliation(s)
- Eric Campeau
- Translational Biology Group, Calgary, AB, Canada.
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29
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Döring Y, Noels H, Weber C. The Use of High-Throughput Technologies to Investigate Vascular Inflammation and Atherosclerosis. Arterioscler Thromb Vasc Biol 2012; 32:182-95. [DOI: 10.1161/atvbaha.111.232686] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The greatest challenge of scientific research is to understand the causes and consequences of disease. In recent years, great efforts have been devoted to unraveling the basic mechanisms of atherosclerosis (the underlying pathology of cardiovascular disease), which remains a major cause of morbidity and mortality worldwide. Because of the complex and multifactorial pathophysiology of cardiovascular disease, different research techniques have increasingly been combined to unravel genetic aspects, molecular pathways, and cellular functions involved in atherogenesis, vascular inflammation, and dyslipidemia to gain a multifaceted picture addressing this complexity. Thanks to the rapid evolution of high-throughput technologies, we are now able to generate large-scale data on the DNA, RNA, and protein levels. With the help of sophisticated computational tools, these data sets are integrated to enhance information extraction and are being increasingly used in a systems biology approach to model biological processes as interconnected and regulated networks. This review exemplifies the use of high-throughput technologies—such as genomics, transcriptomics, proteomics, and epigenomics—and systems biology to explore pathomechanisms of vascular inflammation and atherosclerosis.
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Affiliation(s)
- Yvonne Döring
- From the Institute for Cardiovascular Prevention, Ludwig-Maximilians-University Munich, Munich, Germany (Y.D., C.W.); Institute for Molecular Cardiovascular Research, Rheinisch-Westfälische Technische Hochschule Aachen University, University Clinic Aachen, Aachen, Germany (H.N.); Munich Heart Alliance, Munich, Germany (C.W.); Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, the Netherlands (C.W.)
| | - Heidi Noels
- From the Institute for Cardiovascular Prevention, Ludwig-Maximilians-University Munich, Munich, Germany (Y.D., C.W.); Institute for Molecular Cardiovascular Research, Rheinisch-Westfälische Technische Hochschule Aachen University, University Clinic Aachen, Aachen, Germany (H.N.); Munich Heart Alliance, Munich, Germany (C.W.); Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, the Netherlands (C.W.)
| | - Christian Weber
- From the Institute for Cardiovascular Prevention, Ludwig-Maximilians-University Munich, Munich, Germany (Y.D., C.W.); Institute for Molecular Cardiovascular Research, Rheinisch-Westfälische Technische Hochschule Aachen University, University Clinic Aachen, Aachen, Germany (H.N.); Munich Heart Alliance, Munich, Germany (C.W.); Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, the Netherlands (C.W.)
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30
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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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31
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Abstract
RNA interference (RNAi) is an experimental technique used to suppress individual gene expression in eukaryotic cells in a sequence-dependent manner. The process relies on double-stranded RNA (dsRNA) to target complementary messenger RNA for degradation. Here, we describe two plasmid-based strategies we have developed for RNAi in Cryptococcus neoformans. The pFrame vector utilizes the ACT1 promoter to enable the constitutive synthesis of hairpin RNA (hpRNA), the stem of which constitutes the dsRNA trigger. The pIBB103 vector relies on convergent, inducible GAL7 promoters to independently drive the synthesis of the sense and antisense strands of the interfering sequence; these strands anneal to form the initiating dsRNA molecule. Both vectors are designed to co-silence a "sentinel" gene with an easily scored phenotype to help identify clones in which RNAi is most effective. We provide guidelines for selecting a suitable interfering sequence to trigger RNAi in C. neoformans and describe the steps for subcloning into either vector, transforming C. neoformans by electroporation, screening clones for RNAi-related phenotypes, and evaluating the efficacy and specificity of gene silencing by RNAi.
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32
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Gilbert DF, Erdmann G, Zhang X, Fritzsche A, Demir K, Jaedicke A, Muehlenberg K, Wanker EE, Boutros M. A novel multiplex cell viability assay for high-throughput RNAi screening. PLoS One 2011; 6:e28338. [PMID: 22162763 PMCID: PMC3230607 DOI: 10.1371/journal.pone.0028338] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Accepted: 11/06/2011] [Indexed: 01/08/2023] Open
Abstract
Cell-based high-throughput RNAi screening has become a powerful research tool in addressing a variety of biological questions. In RNAi screening, one of the most commonly applied assay system is measuring the fitness of cells that is usually quantified using fluorescence, luminescence and absorption-based readouts. These methods, typically implemented and scaled to large-scale screening format, however often only yield limited information on the cell fitness phenotype due to evaluation of a single and indirect physiological indicator. To address this problem, we have established a cell fitness multiplexing assay which combines a biochemical approach and two fluorescence-based assaying methods. We applied this assay in a large-scale RNAi screening experiment with siRNA pools targeting the human kinome in different modified HEK293 cell lines. Subsequent analysis of ranked fitness phenotypes assessed by the different assaying methods revealed average phenotype intersections of 50.7±2.3%–58.7±14.4% when two indicators were combined and 40–48% when a third indicator was taken into account. From these observations we conclude that combination of multiple fitness measures may decrease false-positive rates and increases confidence for hit selection. Our robust experimental and analytical method improves the classical approach in terms of time, data comprehensiveness and cost.
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Affiliation(s)
- Daniel F Gilbert
- German Cancer Research Center (DKFZ), Division of Signaling and Functional Genomics and Heidelberg University, Department of Cell and Molecular Biology, Heidelberg, Germany.
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33
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Mohr SE, Perrimon N. RNAi screening: new approaches, understandings, and organisms. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011; 3:145-58. [PMID: 21953743 DOI: 10.1002/wrna.110] [Citation(s) in RCA: 97] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
RNA interference (RNAi) leads to sequence-specific knockdown of gene function. The approach can be used in large-scale screens to interrogate function in various model organisms and an increasing number of other species. Genome-scale RNAi screens are routinely performed in cultured or primary cells or in vivo in organisms such as C. elegans. High-throughput RNAi screening is benefitting from the development of sophisticated new instrumentation and software tools for collecting and analyzing data, including high-content image data. The results of large-scale RNAi screens have already proved useful, leading to new understandings of gene function relevant to topics such as infection, cancer, obesity, and aging. Nevertheless, important caveats apply and should be taken into consideration when developing or interpreting RNAi screens. Some level of false discovery is inherent to high-throughput approaches and specific to RNAi screens, false discovery due to off-target effects (OTEs) of RNAi reagents remains a problem. The need to improve our ability to use RNAi to elucidate gene function at large scale and in additional systems continues to be addressed through improved RNAi library design, development of innovative computational and analysis tools and other approaches.
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Affiliation(s)
- Stephanie E Mohr
- Drosophila RNAi Screening Center, Department of Genetics, Harvard Medical School, Boston, MA, USA
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34
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Serva A, Claas C, Starkuviene V. A Potential of microRNAs for High-Content Screening. J Nucleic Acids 2011; 2011:870903. [PMID: 21922044 PMCID: PMC3172976 DOI: 10.4061/2011/870903] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2010] [Revised: 05/15/2011] [Accepted: 06/03/2011] [Indexed: 12/19/2022] Open
Abstract
In the last years miRNAs have increasingly been recognised as potent posttranscriptional regulators of gene expression. Possibly, miRNAs exert their action on virtually any biological process by simultaneous regulation of numerous genes. The importance of miRNA-based regulation in health and disease has inspired research to investigate diverse aspects of miRNA origin, biogenesis, and function. Despite the recent rapid accumulation of experimental data, and the emergence of functional models, the complexity of miRNA-based regulation is still far from being well understood. In particular, we lack comprehensive knowledge as to which cellular processes are regulated by which miRNAs, and, furthermore, how temporal and spatial interactions of miRNAs to their targets occur. Results from large-scale functional analyses have immense potential to address these questions. In this review, we discuss the latest progress in application of high-content and high-throughput functional analysis for the systematic elucidation of the biological roles of miRNAs.
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Affiliation(s)
- Andrius Serva
- BioQuant, University of Heidelberg, 69120 Heidelberg, Germany
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35
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Screening of siRNA nanoparticles for delivery to airway epithelial cells using high-content analysis. Ther Deliv 2011; 2:987-99. [DOI: 10.4155/tde.11.73] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Aims: Delivery of siRNA to the lungs via inhalation offers a unique opportunity to develop a new treatment paradigm for a range of respiratory conditions. However, progress has been greatly hindered by safety and delivery issues. This study developed a high-throughput method for screening novel nanotechnologies for pulmonary siRNA delivery. Methodology: Following physicochemical analysis, the ability of PEI–PEG–siRNA nanoparticles to facilitate siRNA delivery was determined using high-content analysis (HCA) in Calu-3 cells. Results obtained from HCA were validated using confocal microscopy. Finally, cytotoxicity of the PEI–PEG–siRNA particles was analyzed by HCA using the Cellomics® multiparameter cytotoxicity assay. Conclusion: PEI–PEG–siRNA nanoparticles facilitated increased siRNA uptake and luciferase knockdown in Calu-3 cells compared with PEI–siRNA.
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36
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Jiang M, Instrell R, Saunders B, Berven H, Howell M. Tales from an academic RNAi screening facility; FAQs. Brief Funct Genomics 2011; 10:227-37. [PMID: 21527443 DOI: 10.1093/bfgp/elr016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
RNAi technology is now a well-established and widely employed research technique that has been adopted by many researchers for use in large-scale screening campaigns. Here, we offer our experience of genome-wide siRNA screening from the perspective of a facility providing screening as a service to a wide range of researchers with diverse interests and approaches. We have experienced the emotional rollercoaster of screening from the exuberant early promise of a screen, the messy reality of the data through to the recognition of screen data as a potential information goldmine. Here, we use some of the questions we most frequently encounter to highlight the initial concerns of many researchers embarking on a siRNA screen and conclude that an informed view of what can be reasonably expected from a screen is essential to the most effective implementation of the technology. Along the way, we suggest that for this area of research at least, either centralization of the resources or close and open collaboration between interested parties offers distinct advantages.
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Affiliation(s)
- Ming Jiang
- High-Throughput Screening facility, Cancer Research UK, London Research Institute
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Ehlgen F, Riglar D. Meeting report: Practical course in imaging and microscopy. Biotechnol J 2010; 5:1253-6. [PMID: 21154728 DOI: 10.1002/biot.201000374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Genome-wide RNAi screens in bloodstream form trypanosomes identify drug transporters. Mol Biochem Parasitol 2010; 175:91-4. [PMID: 20851719 DOI: 10.1016/j.molbiopara.2010.09.002] [Citation(s) in RCA: 161] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2010] [Revised: 09/03/2010] [Accepted: 09/08/2010] [Indexed: 11/23/2022]
Abstract
An inducible RNA interference (RNAi) library, consisting of a pool of independent stable transformants with 9-fold genome coverage, was constructed in bloodstream form Trypanosoma brucei using an improved transfection protocol. RNAi induction and selection of resistant parasites was performed in the presence of melarsoprol or eflornithine. The former led to the isolation of the adenosine transporter TbAT1, which is known to be involved in melarsoprol uptake, while the latter identified an amino acid transporter, AAT6. Knockdown of AAT6 reduced mRNA levels to 30-35% in independent clones and increased resistance to eflornithine >5-fold. Genome-wide screens with this library allow an unbiased approach to gene discovery, are extremely rapid and do not exclude essential genes.
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Janssens B. Editorial: From β-catenin and signaling to biotech. Biotechnol J 2010; 5:343. [DOI: 10.1002/biot.201000056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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