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Güneş C, Paszkowski-Rogacz M, Rahmig S, Khattak S, Camgöz A, Wermke M, Dahl A, Bornhäuser M, Waskow C, Buchholz F. Comparative RNAi Screens in Isogenic Human Stem Cells Reveal SMARCA4 as a Differential Regulator. Stem Cell Reports 2019; 12:1084-1098. [PMID: 31031192 PMCID: PMC6523874 DOI: 10.1016/j.stemcr.2019.03.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 03/26/2019] [Accepted: 03/27/2019] [Indexed: 12/20/2022] Open
Abstract
Large-scale RNAi screens are a powerful approach to identify functions of genes in a cell-type-specific manner. For model organisms, genetically identical (isogenic) cells from different cell types are readily available, making comparative studies meaningful. However, large-scale screens in isogenic human primary cells remain challenging. Here, we show that RNAi screens are possible in genetically identical human stem cells, using induced pluripotent stem cells as intermediates. The screens revealed SMARCA4 (SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4) as a stemness regulator, while balancing differentiation distinctively for each cell type. SMARCA4 knockdown in hematopoietic stem and progenitor cells caused impaired self-renewal in vitro and in vivo with skewed myeloid differentiation; whereas, in neural stem cells, it impaired self-renewal while biasing differentiation toward neural lineage, through combinatorial SWI/SNF subunit assembly. Our findings pose a powerful approach for deciphering human stem cell biology and attribute distinct roles to SMARCA4 in stem cell maintenance. Comparative RNAi screens on isogenic hHSPCs and hNSCs, using iPSCs as bridging cell type SMARCA4 is a differential regulator of self-renewal and differentiation SMARCA4 loss impairs HSPC engraftment in vivo and myeloid differentiation in vitro SMARCA4 loss in NSCs causes exit from self-renewal and biased neural differentiation
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Affiliation(s)
- Ceren Güneş
- Medical Faculty and University Hospital Carl Gustav Carus, UCC Section Medical Systems Biology, TU Dresden, 01307 Dresden, Germany
| | - Maciej Paszkowski-Rogacz
- Medical Faculty and University Hospital Carl Gustav Carus, UCC Section Medical Systems Biology, TU Dresden, 01307 Dresden, Germany
| | - Susann Rahmig
- Regeneration in Hematopoiesis, Leibniz Institute on Aging - Fritz Lipmann Institute, 07745 Jena, Germany
| | - Shahryar Khattak
- Stem Cell Engineering Facility, Biotechnology Center, TU Dresden, 01307 Dresden, Germany
| | - Aylin Camgöz
- Medical Faculty and University Hospital Carl Gustav Carus, UCC Section Medical Systems Biology, TU Dresden, 01307 Dresden, Germany; National Center for Tumor Diseases (NCT), University Hospital Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany
| | - Martin Wermke
- Department of Medicine I, University Hospital Carl Gustav Carus, 01307 Dresden, Germany; Medical Faculty and University Hospital Carl Gustav Carus, Early Clinical Trial Unit, 01307 Dresden, Germany
| | - Andreas Dahl
- Dresden Genome Center (DGC), TU Dresden, 01307 Dresden, Germany
| | - Martin Bornhäuser
- Department of Medicine I, University Hospital Carl Gustav Carus, 01307 Dresden, Germany
| | - Claudia Waskow
- Regeneration in Hematopoiesis, Leibniz Institute on Aging - Fritz Lipmann Institute, 07745 Jena, Germany; Department of Medicine III, Faculty of Medicine, Fetscherstrasse 74, 01307 Dresden, Germany
| | - Frank Buchholz
- Medical Faculty and University Hospital Carl Gustav Carus, UCC Section Medical Systems Biology, TU Dresden, 01307 Dresden, Germany; German Cancer Research Center (DKFZ), Heidelberg and German Research Consortium (DKTK), Partner Site Dresden, 01307 Dresden, Germany; National Center for Tumor Diseases (NCT), University Hospital Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany; Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany.
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Genome-wide piggyBac transposon mediated screening reveals genes related to reprogramming. Protein Cell 2016; 8:134-139. [PMID: 27761808 PMCID: PMC5291772 DOI: 10.1007/s13238-016-0332-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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Abstract
RNAi technologies enable the testing of gene function in a cell-type- and stage-specific manner in Drosophila. The development of genome-wide RNAi libraries has allowed expansion of this approach to the genome scale and supports identification of most genes required for a given process in a cell type of choice. However, a large-scale RNAi approach also harbors many potential pitfalls that can complicate interpretation of the results. Here, we summarize published screens and provide a guide on how to optimally plan and perform a large-scale, in vivo RNAi screen. We highlight the importance of assay design and give suggestions on how to optimize the assay conditions by testing positive and negative control genes. These genes are used to estimate false-negative and false-positive rates of the screen data. We discuss the planning and logistics of a large-scale screen in detail and suggest bioinformatics platforms to identify and select gene groups of interest for secondary assays. Finally, we review various options to confirm RNAi knock-down specificity and thus identify high confidence genes for more detailed case-by-case studies in the future.
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Systems Analyses Reveal Shared and Diverse Attributes of Oct4 Regulation in Pluripotent Cells. Cell Syst 2015; 1:141-51. [PMID: 27135800 DOI: 10.1016/j.cels.2015.08.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 07/07/2015] [Accepted: 08/04/2015] [Indexed: 11/23/2022]
Abstract
We combine a genome-scale RNAi screen in mouse epiblast stem cells (EpiSCs) with genetic interaction, protein localization, and "protein-level dependency" studies-a systematic technique that uncovers post-transcriptional regulation-to delineate the network of factors that control the expression of Oct4, a key regulator of pluripotency. Our data signify that there are similarities, but also fundamental differences in Oct4 regulation in EpiSCs versus embryonic stem cells (ESCs). Through multiparametric data analyses, we predict that Tox4 is associating with the Paf1C complex, which maintains cell identity in both cell types, and validate that this protein-protein interaction exists in ESCs and EpiSCs. We also identify numerous knockdowns that increase Oct4 expression in EpiSCs, indicating that, in stark contrast to ESCs, Oct4 is under active repressive control in EpiSCs. These studies provide a framework for better understanding pluripotency and for dissecting the molecular events that govern the transition from the pre-implantation to the post-implantation state.
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Dubrovska A. Report on the International Workshop 'Cancer stem cells: the mechanisms of radioresistance and biomarker discovery'. Int J Radiat Biol 2014; 90:607-14. [PMID: 24844377 DOI: 10.3109/09553002.2014.920968] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The aim of the Workshop "Cancer stem cells: The mechanisms of radioresistance and biomarker discovery", which was held on 23-24 September 2013 at OncoRay - National Center for Radiation Research in Oncology in Dresden, Germany, was to bring together the most recent viewpoints and insights about: (i) the molecular characterization and regulation of CSC, (ii) the mechanisms of CSC radioresistance, and (iii) the discovery of new CSC targeting therapeutics and biomarkers. In this report some research aspects presented in these three topics are highlighted.
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Affiliation(s)
- Anna Dubrovska
- OncoRay - National Center for Radiation Research in Oncology, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden and Helmholtz-Zentrum Dresden-Rossendorf, Dresden , German Cancer Consortium (DKTK) Dresden, and German Cancer Research Center (DKFZ) Heidelberg , Germany
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Mäbert K, Cojoc M, Peitzsch C, Kurth I, Souchelnytskyi S, Dubrovska A. Cancer biomarker discovery: current status and future perspectives. Int J Radiat Biol 2014; 90:659-77. [PMID: 24524284 DOI: 10.3109/09553002.2014.892229] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
PURPOSE Cancer is a multigene disease which arises as a result of mutational and epigenetic changes coupled with activation of complex signaling networks. The use of biomarkers for early cancer detection, staging and individualization of therapy might improve patient care. A few fundamental issues such as tumor heterogeneity, a highly dynamic nature of the intrinsic and extrinsic determinants of radio- and chemoresistance, along with the plasticity and diversity of cancer stem cells (CSC) make biomarker development a challenging task. In this review we outline the preclinical strategies of cancer biomarker discovery including genomic, proteomic, metabolomic and microRNomic profiling, comparative genome hybridization (CGH), single nucleotide polymorphism (SNP) analysis, high throughput screening (HTS) and next generation sequencing (NGS). Other promising approaches such as assessment of circulating tumor cells (CTC), analysis of CSC-specific markers and cell-free circulating tumor DNA (ctDNA) are also discussed. CONCLUSIONS The emergence of powerful proteomic and genomic technologies in conjunction with advanced bioinformatic tools allows the simultaneous analysis of thousands of biological molecules. These techniques yield the discovery of new tumor signatures, which are sensitive and specific enough for early cancer detection, for monitoring disease progression and for proper treatment selection, paving the way to individualized cancer treatment.
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Affiliation(s)
- Katrin Mäbert
- OncoRay-National Center for Radiation Research in Oncology, Medical Faculty Dresden Carl Gustav Carus , TU Dresden , Germany
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Abstract
Much of what is known about mammalian cell regulation has been achieved with the aid of transiently transfected cells. However, overexpression can violate balanced gene dosage, affecting protein folding, complex assembly and downstream regulation. To avoid these problems, genome engineering technologies now enable the generation of stable cell lines expressing modified proteins at (almost) native levels.
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Affiliation(s)
- Toby J Gibson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
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Peitzsch C, Kurth I, Kunz-Schughart L, Baumann M, Dubrovska A. Discovery of the cancer stem cell related determinants of radioresistance. Radiother Oncol 2013; 108:378-87. [PMID: 23830195 DOI: 10.1016/j.radonc.2013.06.003] [Citation(s) in RCA: 133] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 05/31/2013] [Accepted: 06/05/2013] [Indexed: 12/23/2022]
Abstract
Tumors are known to be heterogeneous containing a dynamic mixture of phenotypically and functionally different tumor cells. The two concepts attempting to explain the origin of intratumor heterogeneity are the cancer stem cell hypothesis and the clonal evolution model. The stochastic model argues that tumors are biologically homogenous and all cancer cells within the tumor have equal ability to propagate the tumor growth depending on continuing mutations and selective pressure. By contrast, the stem cells model suggests that cancer heterogeneity is due to the hierarchy that originates from a small population of cancer stem cells (CSCs) which are biologically distinct from the bulk tumor and possesses self-renewal, tumorigenic and multilineage potential. Although these two hypotheses have been discussed for a long time as mutually exclusive explanations of tumor heterogeneity, they are easily reconciled serving as a driving force of cancer evolution and diversity. Recent discovery of the cancer cell plasticity and heterogeneity makes the CSC population a moving target that could be hard to track and eradicate. Understanding the signaling mechanisms regulating CSCs during the course of cancer treatment can be indispensable for the optimization of current treatment strategies.
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Affiliation(s)
- Claudia Peitzsch
- OncoRay National Center for Radiation Research in Oncology, University Hospital/Medical Faculty Carl Gustav Carus, TU Dresden, Germany
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Automated high-throughput RNAi screening in human cells combined with reporter mRNA transfection to identify novel regulators of translation. PLoS One 2012; 7:e45943. [PMID: 23029333 PMCID: PMC3459937 DOI: 10.1371/journal.pone.0045943] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Accepted: 08/23/2012] [Indexed: 12/21/2022] Open
Abstract
Proteins that promote angiogenesis, such as vascular endothelial growth factor (VEGF), are major targets for cancer therapy. Accordingly, proteins that specifically activate expression of factors like VEGF are potential alternative therapeutic targets and may help to combat evasive resistance to angiogenesis inhibitors. VEGF mRNA contains two internal ribosome entry sites (IRESs) that enable selective activation of VEGF protein synthesis under hypoxic conditions that trigger angiogenesis. To identify novel regulators of VEGF IRES-driven translation in human cells, we have developed a high-throughput screening approach that combines siRNA treatment with transfection of a VEGF-IRES reporter mRNA. We identified the kinase MAPK3 as a novel positive regulator of VEGF IRES-driven translation and have validated its regulatory effect on endogenous VEGF. Our automated method is scalable and readily adapted for use with other mRNA regulatory elements. Consequently, it should be a generally useful approach for high-throughput identification of novel regulators of mRNA translation.
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Abstract
Genetics has fascinated societies since ancient times, and references to traits or behaviors that appear to be shared or different among related individuals have permeated legends, literature, and popular culture. Biomedical advances from the past century, and particularly the discovery of the DNA double helix, the increasing numbers of links that were established between mutations and medical conditions or phenotypes, and technological advances that facilitated the sequencing of the human genome, catalyzed the development of genetic testing. Genetic tests were initially performed in health care facilities, interpreted by health care providers, and included the availability of counseling. Recent years have seen an increased availability of genetic tests that are offered by companies directly to consumers, a phenomenon that became known as direct-to-consumer genetic testing. Tests offered in this setting range from the ones that are also provided in health care establishments to tests known as ‘recreational genomics,’ and consumers directly receive the test results. In addition, testing in this context often does not involve the availability of counseling and, when this is provided, it frequently occurs on-line or over the phone. As a field situated at the interface between biotechnology, biomedical research, and social sciences, direct-to-consumer genetic testing opens multiple challenges that can be appropriately addressed only by developing a complex, inter-disciplinary framework.
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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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