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Peng Y, Li Z, Chen S, Zhou J. DHFR silence alleviated the development of liver fibrosis by affecting the crosstalk between hepatic stellate cells and macrophages. J Cell Mol Med 2021; 25:10049-10060. [PMID: 34626074 PMCID: PMC8572769 DOI: 10.1111/jcmm.16935] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 08/26/2021] [Accepted: 09/01/2021] [Indexed: 01/20/2023] Open
Abstract
Liver fibrogenesis is a dynamic cellular and tissue process which has the potential to progress into cirrhosis of even liver cancer and liver failure. The activation of hepatic stellate cells (HSCs) is the central event underlying liver fibrosis. Besides, hepatic macrophages have been proposed as potential targets in combatting fibrosis. As for the relationship between HSCs and hepatic macrophages in liver fibrosis, it is generally considered that macrophages promoted liver fibrosis via activating HSCs. However, whether activated HSCs could in turn affect macrophage polarization has rarely been studied. In this study, mRNAs with significant differences were explored using exosomal RNA‐sequencing of activated Lx‐2 cells and normal RNA‐sequencing of DHFR loss‐of‐function Lx‐2 cell models. Cell functional experiments in both Lx‐2 cells and macrophages animal model experiments were performed. The results basically confirmed exosomes secreted from activated HSCs could promote M1 polarization of macrophages further. Exosome harbouring DHFR played an important role in this process. DHFR silence in HSCs could decrease Lx‐2 activation and M1 polarization of M0 macrophages and then alleviate the development of liver fibrosis both in vitro and vivo. Our work brought a new insight that exosomal DHFR derived from HSCs had a crucial role in crosstalk between HSCs activation and macrophage polarization, which may be a potential therapeutic target in liver fibrosis.
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Affiliation(s)
- Yu Peng
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Zedong Li
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Sheng Chen
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Jun Zhou
- Department of Emergency Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
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2
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Human dihydrofolate reductase is a substrate of protein kinase CK2α. Biochem Biophys Res Commun 2019; 513:368-373. [PMID: 30961929 DOI: 10.1016/j.bbrc.2019.03.186] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 03/27/2019] [Indexed: 11/22/2022]
Abstract
Dihydrofolate reductase (DHFR) is a prominent molecular target in antitumor, antibacterial, antiprotozoan, and immunosuppressive chemotherapies, and CK2 protein kinase is an ubiquitous enzyme involved in many processes, such as tRNA and rRNA synthesis, apoptosis, cell cycle or oncogenic transformation. We show for the first time that CK2α subunit strongly interacted with and phosphorylated DHFR in vitro. Using quartz crystal microbalance with dissipation monitoring (QCM-D) we determined DHFR-CK2α binding kinetic parameters (Kd below 0.5 μM, kon = 10.31 × 104 M-1s-1 and koff = 1.40 × 10-3s-1) and calculated Gibbs free energy (-36.4 kJ/mol). In order to identify phosphorylation site(s) we used site-directed mutagenesis to obtain several DHFR mutants with predicted CK2-phosphorylable serine or threonine residues substituted with alanines. All enzyme forms were subjected to CK2α subunit catalytic activity and the results pointed to serine 168 as a phosphorylation site. Mass spectrometry analyses confirmed the presence of phosphoserine 168 and revealed additionally the presence of phosphoserine 145, although the latter phosphorylation was on a very low level.
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Aguiar S, van der Gaag B, Cortese FAB. RNAi mechanisms in Huntington's disease therapy: siRNA versus shRNA. Transl Neurodegener 2017; 6:30. [PMID: 29209494 PMCID: PMC5702971 DOI: 10.1186/s40035-017-0101-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 10/30/2017] [Indexed: 12/19/2022] Open
Abstract
Huntington's Disease (HD) is a genetically dominant trinucleotide repeat disorder resulting from CAG repeats within the Huntingtin (HTT) gene exceeding a normal range (> 36 CAGs). Symptoms of the disease manifest in middle age and include chorea, dystonia, and cognitive decline. Typical latency from diagnosis to death is 20 years. There are currently no disease-modifying therapies available to HD patients. RNAi is a potentially curative therapy for HD. A popular line of research employs siRNA or antisense oligonucleotides (ASO) to knock down mutant Huntingtin mRNA (mHTT). Unfortunately, this modality requires repeated dosing, commonly exhibit off target effects (OTEs), and exert renal and hepatic toxicity. In contrast, a single AAV-mediated short-hairpin RNA (shRNA) dose can last years with low toxicity. In addition, we highlight research indicating that shRNA elicits fewer OTEs than siRNA when tested head-to-head. Despite this promise, shRNA therapy has been held back by difficulties controlling expression (oversaturating cells with toxic levels of RNA construct). In this review, we compare RNAi modalities for HD and propose novel methods of optimizing shRNA expression and on-target fidelity.
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Affiliation(s)
- Sebastian Aguiar
- Molecular Neuroscience Laboratory, Swammerdam Institute for Life Sciences (SILS-CNS), University of Amsterdam, Amsterdam, Netherlands
- Fulbright Program, US Department of State (IIE), New York City, NY USA
| | - Bram van der Gaag
- Molecular Neuroscience Laboratory, Swammerdam Institute for Life Sciences (SILS-CNS), University of Amsterdam, Amsterdam, Netherlands
- Department of Neurobiology, Care Sciences and Society, Karolinska Institute, Stockholm, Sweden
| | - Francesco Albert Bosco Cortese
- Biogerontology Research Foundation (BGRF), Oxford, UK
- Department of Biomedical and Molecular Sciences, Queen’s University School of Medicine, Queen’s University, Kingston, Canada
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Lee JA, Shinn P, Jaken S, Oliver S, Willard FS, Heidler S, Peery RB, Oler J, Chu S, Southall N, Dexheimer TS, Smallwood J, Huang R, Guha R, Jadhav A, Cox K, Austin CP, Simeonov A, Sittampalam GS, Husain S, Franklin N, Wild DJ, Yang JJ, Sutherland JJ, Thomas CJ. Novel Phenotypic Outcomes Identified for a Public Collection of Approved Drugs from a Publicly Accessible Panel of Assays. PLoS One 2015; 10:e0130796. [PMID: 26177200 PMCID: PMC4503722 DOI: 10.1371/journal.pone.0130796] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 05/26/2015] [Indexed: 12/17/2022] Open
Abstract
Phenotypic assays have a proven track record for generating leads that become first-in-class therapies. Whole cell assays that inform on a phenotype or mechanism also possess great potential in drug repositioning studies by illuminating new activities for the existing pharmacopeia. The National Center for Advancing Translational Sciences (NCATS) pharmaceutical collection (NPC) is the largest reported collection of approved small molecule therapeutics that is available for screening in a high-throughput setting. Via a wide-ranging collaborative effort, this library was analyzed in the Open Innovation Drug Discovery (OIDD) phenotypic assay modules publicly offered by Lilly. The results of these tests are publically available online at www.ncats.nih.gov/expertise/preclinical/pd2 and via the PubChem Database (https://pubchem.ncbi.nlm.nih.gov/) (AID 1117321). Phenotypic outcomes for numerous drugs were confirmed, including sulfonylureas as insulin secretagogues and the anti-angiogenesis actions of multikinase inhibitors sorafenib, axitinib and pazopanib. Several novel outcomes were also noted including the Wnt potentiating activities of rotenone and the antifolate class of drugs, and the anti-angiogenic activity of cetaben.
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Affiliation(s)
- Jonathan A. Lee
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana, United States of America
| | - Paul Shinn
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Susan Jaken
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana, United States of America
| | - Sarah Oliver
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana, United States of America
| | - Francis S. Willard
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana, United States of America
| | - Steven Heidler
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana, United States of America
| | - Robert B. Peery
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana, United States of America
| | - Jennifer Oler
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana, United States of America
| | - Shaoyou Chu
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana, United States of America
| | - Noel Southall
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Thomas S. Dexheimer
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Jeffrey Smallwood
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana, United States of America
| | - Ruili Huang
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Rajarshi Guha
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Ajit Jadhav
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Karen Cox
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana, United States of America
| | - Christopher P. Austin
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Anton Simeonov
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland, United States of America
| | - G. Sitta Sittampalam
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Saba Husain
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana, United States of America
| | - Natalie Franklin
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana, United States of America
| | - David J. Wild
- Indiana University School of Informatics and Computing, Bloomington, Indiana, United States of America
| | - Jeremy J. Yang
- Indiana University School of Informatics and Computing, Bloomington, Indiana, United States of America
| | - Jeffrey J. Sutherland
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana, United States of America
- * E-mail: (JJS); (CJT)
| | - Craig J. Thomas
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail: (JJS); (CJT)
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5
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Wylie PG, Onley DJ, Hammerstein AF, Bowen WP. Advances in Laser Scanning Imaging Cytometry for High-Content Screening. Assay Drug Dev Technol 2015; 13:66-78. [DOI: 10.1089/adt.2014.607] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- Paul G. Wylie
- TTP Labtech Limited, Melbourn, Hertfordshire, United Kingdom
| | - David J. Onley
- TTP Labtech Limited, Melbourn, Hertfordshire, United Kingdom
| | | | - Wayne P. Bowen
- TTP Labtech Limited, Melbourn, Hertfordshire, United Kingdom
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6
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Vu-Phan D, Grachtchouk V, Yu J, Colby LA, Wicha MS, Koenig RJ. The thyroid cancer PAX8-PPARG fusion protein activates Wnt/TCF-responsive cells that have a transformed phenotype. Endocr Relat Cancer 2013; 20:725-39. [PMID: 24025583 PMCID: PMC3839064 DOI: 10.1530/erc-13-0058] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A chromosomal translocation results in the production of a paired box 8-peroxisome proliferator-activated receptor gamma (PAX8-PPARG) fusion protein (PPFP) in ∼35% of follicular thyroid carcinomas. To examine the role of PPFP in thyroid oncogenesis, the fusion protein was stably expressed in the non-transformed rat thyroid cell line PCCL3. PPFP conferred on PCCL3 cells the ability to invade through Matrigel and to form colonies in anchorage-independent conditions. PPFP also increased the fraction of cells with Wnt/TCF-responsive green fluorescent protein reporter gene expression. This Wnt/TCF-activated population was enriched for colony-forming and invading cells. These actions of PPFP required a functional PPARG DNA binding domain (DBD) within PPFP and were further stimulated by PPARG agonists. These data indicate that PPFP, through its PPARG DBD, induces Wnt/TCF pathway activation in a subpopulation of cells, and these cells have properties of cellular transformation including increased invasiveness and anchorage-independent growth.
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Affiliation(s)
- Dang Vu-Phan
- Cellular and Molecular Biology Graduate Program, Department of Internal Medicine, University of Michigan Medical Center, Ann Arbor, 48109, USA
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7
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Segura MM, Mangion M, Gaillet B, Garnier A. New developments in lentiviral vector design, production and purification. Expert Opin Biol Ther 2013; 13:987-1011. [PMID: 23590247 DOI: 10.1517/14712598.2013.779249] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Lentiviruses are a very potent class of viral vectors for which there is presently a rapidly growing interest for a number of gene therapy. However, their construction, production and purification need to be performed according to state-of-the-art techniques in order to obtain sufficient quantities of high purity material of any usefulness and safety. AREAS COVERED The recent advances in the field of recombinant lentivirus vector design, production and purification will be reviewed with an eye toward its utilization for gene therapy. Such a review should be helpful for the potential user of this technology. EXPERT OPINION The principal hurdles toward the use of recombinant lentivirus as a gene therapy vector are the low titer at which it is produced as well as the difficulty to purify it at an acceptable level without degrading it. The recent advances in the bioproduction of this vector suggest these issues are about to be resolved, making the retrovirus gene therapy a mature technology.
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Affiliation(s)
- Maria Mercedes Segura
- Chemical Engineering Department, Universitat Autònoma de Barcelona, Campus Bellaterra, Cerdanyola del Vallès (08193), Barcelona, Spain
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8
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Zhang XD, Heyse JF. Contrast Variable for Group Comparisons in Biopharmaceutical Research. Stat Biopharm Res 2012. [DOI: 10.1080/19466315.2011.646905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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10
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Zhang XD, Santini F, Lacson R, Marine SD, Wu Q, Benetti L, Yang R, McCampbell A, Berger JP, Toolan DM, Stec EM, Holder DJ, Soper KA, Heyse JF, Ferrer M. cSSMD: assessing collective activity for addressing off-target effects in genome-scale RNA interference screens. ACTA ACUST UNITED AC 2011; 27:2775-81. [PMID: 21846737 DOI: 10.1093/bioinformatics/btr474] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
MOTIVATION Off-target activity commonly exists in RNA interference (RNAi) screens and often generates false positives. Existing analytic methods for addressing the off-target effects are demonstrably inadequate in RNAi confirmatory screens. RESULTS Here, we present an analytic method assessing the collective activity of multiple short interfering RNAs (siRNAs) targeting a gene. Using this method, we can not only reduce the impact of off-target activities, but also evaluate the specific effect of an siRNA, thus providing information about potential off-target effects. Using in-house RNAi screens, we demonstrate that our method obtains more reasonable and sensible results than current methods such as the redundant siRNA activity (RSA) method, the RNAi gene enrichment ranking (RIGER) method, the frequency approach and the t-test. CONTACT xiaohua_zhang@merck.com SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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11
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Blakely K, Ketela T, Moffat J. Pooled lentiviral shRNA screening for functional genomics in mammalian cells. Methods Mol Biol 2011; 781:161-182. [PMID: 21877282 DOI: 10.1007/978-1-61779-276-2_9] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Genome sequencing efforts have reformed the nature of biological inquiry, prompting the development of technologies for the functional annotation of mammalian genes. Based on methodologies originally discovered in plants and Caenorhabditis elegans, RNA interference has offered cell biologists an effective and reproducible approach to perturb gene function in mammalian cells and whole organisms. Initial application of RNA interference libraries targeting the human and mouse genomes relied on arrayed screening approaches, whereby each unique RNA interference reagent is arrayed into individual wells of a microtiter plate. These screens are not trivial to perform, requiring a substantial investment in infrastructure. In the past decade, many technological advances have been made that make genome-wide RNA interference screening more accessible to researchers and more feasible to perform in nonspecialized laboratories. Here, we describe a comprehensive protocol for pooled short-hairpin RNA screening, including methodologies for pooled lentivirus production, cell infection, genome-wide negative selection screening and resources for pooled screen deconvolution, and data analysis. As a technique, pooled shRNA screening is still in its infancy, but the methodology has already been successfully applied to probe diverse signaling pathways, as a means of drug target identification, and to identify essential genes in normal and cancer cell lines.
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Affiliation(s)
- Kim Blakely
- Donnelly Centre and Banting & Best Department of Medical Research, University of Toronto, Toronto, ON, Canada
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12
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Zhang XD, Lacson R, Yang R, Marine SD, McCampbell A, Toolan DM, Hare TR, Kajdas J, Berger JP, Holder DJ, Heyse JF, Ferrer M. The use of SSMD-based false discovery and false nondiscovery rates in genome-scale RNAi screens. ACTA ACUST UNITED AC 2010; 15:1123-31. [PMID: 20852024 DOI: 10.1177/1087057110381919] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
In genome-scale RNA interference (RNAi) screens, it is critical to control false positives and false negatives statistically. Traditional statistical methods for controlling false discovery and false nondiscovery rates are inappropriate for hit selection in RNAi screens because the major goal in RNAi screens is to control both the proportion of short interfering RNAs (siRNAs) with a small effect among selected hits and the proportion of siRNAs with a large effect among declared nonhits. An effective method based on strictly standardized mean difference (SSMD) has been proposed for statistically controlling false discovery rate (FDR) and false nondiscovery rate (FNDR) appropriate for RNAi screens. In this article, the authors explore the utility of the SSMD-based method for hit selection in RNAi screens. As demonstrated in 2 genome-scale RNAi screens, the SSMD-based method addresses the unmet need of controlling for the proportion of siRNAs with a small effect among selected hits, as well as controlling for the proportion of siRNAs with a large effect among declared nonhits. Furthermore, the SSMD-based method results in reasonably low FDR and FNDR for selecting inhibition or activation hits. This method works effectively and should have a broad utility for hit selection in RNAi screens with replicates.
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13
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Gonçalves MAFV, Janssen JM, Holkers M, de Vries AAF. Rapid and sensitive lentivirus vector-based conditional gene expression assay to monitor and quantify cell fusion activity. PLoS One 2010; 5:e10954. [PMID: 20532169 PMCID: PMC2880594 DOI: 10.1371/journal.pone.0010954] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2009] [Accepted: 05/12/2010] [Indexed: 11/18/2022] Open
Abstract
Cell-to-cell fusion is involved in multiple fundamental biological processes. Prominent examples include osteoclast and giant cell formation, fertilization and skeletal myogenesis which involve macrophage, sperm-egg and myoblast fusion, respectively. Indeed, the importance of cell fusion is underscored by the wide range of homeostatic as well as pathologic processes in which it plays a key role. Therefore, rapid and sensitive systems to trace and measure cell fusion events in various experimental systems are in demand. Here, we introduce a bipartite cell fusion monitoring system based on a genetic switch responsive to the site-specific recombinase FLP. To allow flexible deployment in both dividing as well as non-dividing cell populations, inducer and reporter modules were incorporated in lentivirus vector particles. Moreover, the recombinase-inducible transcription units were designed in such a way as to minimize basal activity and chromosomal position effects in the "off" and "on" states, respectively. The lentivirus vector-based conditional gene expression assay was validated in primary human mesenchymal stem cells and in a differentiation model based on muscle progenitor cells from a Duchenne muscular dystrophy patient using reporter genes compatible with live- and single-cell imaging and with whole population measurements. Using the skeletal muscle cell differentiation model, we showed that the new assay displays low background activity, a 2-log dynamic range, high sensitivity and is amenable to the investigation of cell fusion kinetics. The utility of the bipartite cell fusion monitoring system was underscored by a study on the impact of drug- and RNAi-mediated p38 MAPK inhibition on human myocyte differentiation. Finally, building on the capacity of lentivirus vectors to readily generate transgenic animals the present FLP-inducible system should be adaptable, alone or together with Cre/loxP-based assays, to cell lineage tracing and conditional gene manipulation studies in vivo.
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Affiliation(s)
- Manuel A F V Gonçalves
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands.
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Klinghoffer RA, Magnus J, Schelter J, Mehaffey M, Coleman C, Cleary MA. Reduced seed region-based off-target activity with lentivirus-mediated RNAi. RNA (NEW YORK, N.Y.) 2010; 16:879-884. [PMID: 20348445 PMCID: PMC2856882 DOI: 10.1261/rna.1977810] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2009] [Accepted: 02/01/2010] [Indexed: 05/29/2023]
Abstract
Along with silencing intended target genes, transfected siRNAs regulate numerous unintended transcripts through a mechanism in which the equivalent of a microRNA-like seed region in the siRNA recognizes complementary sequences in transcript 3' UTRs. Amelioration of this off-target silencing would lead to more accurate interpretation of RNA interference (RNAi) experiments and thus greatly enhance their value. We tested whether lentivirus-mediated delivery of shRNA is prone to the sequence-based off-target activity prevalent in siRNA experiments. We compared target gene silencing and overall impact on global gene expression caused by multiple sequences delivered as both transfected siRNAs and lentivirus vector-expressed shRNAs. At equivalent levels of target gene silencing, signatures induced by shRNAs were significantly smaller than those induced by cognate siRNAs and arose less frequently from seed region activity. Interestingly, the low level of seed region-based off-target activity exhibited by shRNAs resulted in down-regulation of transcripts that were largely distinct from those regulated by siRNAs. On the basis of these observations, we recommend lentivirus-mediated RNAi for pathway profiling experiments that measure whole genome transcriptional readouts as well as for large-scale screens when resources for extensive follow up are limited.
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